diff --git a/move_back_scripts/stage/README b/move_back_scripts/stage/README new file mode 100644 index 0000000..cf2ce78 --- /dev/null +++ b/move_back_scripts/stage/README @@ -0,0 +1,21 @@ +#create the list of endllpoints: +# from the command line +select common_name, directory from organism ORDER by common_name; +#get a list of all the organisms +psql-U postgres -d webapollo_2 -c 'select common_name,directory from organism ORDER by common_name;'>organism_list.txt + +#makeaworkingfile +cporganism_list.txtorganism_list.txt2 + + + +#removetheleadingandtrailinglines +nanoorganism_list.txt2 + +#removeextrawhitespacefromthefile +perl-pi-e"s/+//g"organism_list.txt2 + +# the perl script needs ALL spaces removed +perl -pi -e "s/ //g" organism_list.txt2 + + diff --git a/move_back_scripts/stage/make_copy_commands.pl b/move_back_scripts/stage/make_copy_commands.pl new file mode 100644 index 0000000..9550111 --- /dev/null +++ b/move_back_scripts/stage/make_copy_commands.pl @@ -0,0 +1,11 @@ +#!/usr/bin/perl -w + +use strict; + +while (<>){ + $_ =~ m/(\S*)\|(\S*)/; +# print "mkdir $1; cd $1; cp ./$1/* $2/trackList.json; cd .. \n"; + print "cp ../../working/$1/* $2/; \n"; + print "cp ../../css/custom.css $2/; \n"; +} + diff --git a/move_back_scripts/stage/move_conf_files_back.sh b/move_back_scripts/stage/move_conf_files_back.sh new file mode 100644 index 0000000..2500de4 --- /dev/null +++ b/move_back_scripts/stage/move_conf_files_back.sh @@ -0,0 +1,256 @@ +cp ../../working/10_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; +cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; +cp ../../working/11_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; +cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; +cp ../../working/12_-_Onthophagus_taurus_training/* /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/; +cp ../../css/custom.css 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../../css/custom.css /app/data/other_species/megrot/jbrowse/data/; +cp ../../working/Melipona_quadrifasciata/* /app/data/other_species/melqua/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/melqua/jbrowse/data/; +cp ../../working/Microplitis_demolitor/* /app/data/other_species/micdem/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/micdem/jbrowse/data/; +cp ../../working/Neodiprion_lecontei/* /app/data/other_species/neolec/Nlec1.1/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/neolec/Nlec1.1/jbrowse/data/; +cp ../../working/Neodiprion_lecontei_training/* /app/data/other_species/neolec/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/neolec/jbrowse/data/; +cp ../../working/Nicrophorus_vespilloides/* /app/data/other_species/nicves/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/nicves/jbrowse/data/; +cp ../../working/Nylanderia_fulva/* /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/; +cp ../../working/Odontomachus_brunneus/* /app/data/other_species/odobru/Obru_v1/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/odobru/Obru_v1/jbrowse/data/; +cp ../../working/Oncopeltus_fasciatus/* /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; +cp ../../css/custom.css /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; +cp ../../working/Oncopeltus_fasciatus_training/* /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; +cp ../../css/custom.css /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/; +cp ../../working/Onthophagus_taurus/* /app/data/BCM_i5k_pilot/onttau/jbrowse/data/; +cp ../../css/custom.css /app/data/BCM_i5k_pilot/onttau/jbrowse/data/; +cp ../../working/Orussus_abietinus/* /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/; +cp ../../css/custom.css /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/; +cp ../../working/Osmia_lignaria/* /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/; +cp ../../working/Pachypsylla_venusta/* /app/data/BCM_i5k_pilot/pacven/jbrowse/data/; +cp ../../css/custom.css /app/data/BCM_i5k_pilot/pacven/jbrowse/data/; +cp ../../working/Parasteatoda_tepidariorum/* /app/data/BCM_i5k_pilot/partep/jbrowse/data/; +cp ../../css/custom.css /app/data/BCM_i5k_pilot/partep/jbrowse/data/; +cp ../../working/Photinus_pyralis/* /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data/; +cp ../../working/Rhagoletis_zephyria/* /app/data/other_species/rhazep/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/rhazep/jbrowse/data/; +cp ../../working/Rhipicephalus_microplus/* /app/data/other_species/rhimic/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/rhimic/jbrowse/data/; +cp ../../working/Rhyzopertha_dominica/* /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/; +cp ../../working/Saccharomyceseubayanus/* /app/data/other_species/saceub/SEUB3.0/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/saceub/SEUB3.0/jbrowse/data/; +cp ../../working/Tigriopus_californicus/* /app/data/other_species/tigcal/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/tigcal/jbrowse/data/; +cp ../../working/Tribolium_castaneum/* /app/data/other_species/tricas/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/tricas/jbrowse/data/; +cp ../../working/Trichogramma_pretiosum/* /app/data/BCM_i5k_pilot/tripre/jbrowse/data/; +cp ../../css/custom.css /app/data/BCM_i5k_pilot/tripre/jbrowse/data/; +cp ../../working/Varroa_destructor/* /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/; +cp ../../working/Varroa_jacobsoni/* /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/; +cp ../../css/custom.css /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/; diff --git a/move_back_scripts/stage/organism_list.txt b/move_back_scripts/stage/organism_list.txt new file mode 100644 index 0000000..09ae054 --- /dev/null +++ b/move_back_scripts/stage/organism_list.txt @@ -0,0 +1,132 @@ + common_name | directory +------------------------------------+-------------------------------------------------------------- + 10_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 11_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 12_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 13_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 14_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 15_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 16_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 17_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 18_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 19_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 1_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 20_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 21_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 22_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 23_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 24_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 25_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 26_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 27_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 28_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 29_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 2_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 30_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 31_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 32_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 33_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 34_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 35_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 36_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 37_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 38_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 39_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 3_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 40_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 4_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 5_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 6_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 7_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 8_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 9_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + Aethina_tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus_planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois_transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora_glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis_mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia_rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera_cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera_dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera_oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia_tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella_germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus_impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Bombus_terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Bradysia_coprophila | /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data + Catajapyx_aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides_sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus_cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis_capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus_insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex_lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus_hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia_nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma_floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diabrotica_virgifera_training | /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data + Diachasma_alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina_citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina_citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila_biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila_bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila_elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila_eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila_ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila_kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Drosophila_rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila_takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Dufourea_novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera_danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea_mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa_dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora_affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora_affinis_-_training | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius_arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella_occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria_mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris_buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda_laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha_halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis_virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella_duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca_vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella_azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Laodelphax_striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum_albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus_hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa_decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Leptinotarsa_decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Limnephilus_lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta_migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles_reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Mamestra_configurata | /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data + Manduca_sexta | /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data + Mayetiola_destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea_extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile_rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona_quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis_demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion_lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Neodiprion_lecontei_training | /app/data/other_species/neolec/jbrowse/data + Nicrophorus_vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia_fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus_brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus_fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus_fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Onthophagus_taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + Orussus_abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia_lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla_venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda_tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Photinus_pyralis | /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data + Rhagoletis_zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus_microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha_dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Saccharomyces eubayanus | /app/data/other_species/saceub/SEUB3.0/jbrowse/data + Tigriopus_californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium_castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma_pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa_destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Varroa_jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data +(128 rows) + diff --git a/move_back_scripts/stage/organism_list.txt2 b/move_back_scripts/stage/organism_list.txt2 new file mode 100644 index 0000000..54691ba --- /dev/null +++ b/move_back_scripts/stage/organism_list.txt2 @@ -0,0 +1,128 @@ +10_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +11_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +12_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +13_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +14_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +15_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +16_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +17_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +18_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +19_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +1_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +20_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +21_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +22_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +23_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +24_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +25_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +26_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +27_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +28_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +29_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +2_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +30_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +31_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +32_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +33_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +34_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +35_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +36_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +37_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +38_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +39_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +3_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +40_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +4_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +5_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +6_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +7_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +8_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +9_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +Aethina_tumida|/app/data/other_species/aettum/jbrowse/data +Agrilus_planipennis|/app/data/BCM_i5k_pilot/agrpla/jbrowse/data +Amyelois_transitella|/app/data/other_species/amytra/jbrowse/data +Anoplophora_glabripennis|/app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data +Apis_mellifera|/app/data/other_species/apimel/Amel_4.5/jbrowse/data/ +Athalia_rosae|/app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data +Bactrocera_cucurbitae|/app/data/other_species/baccuc/jbrowse/data +Bactrocera_dorsalis|/app/data/other_species/bacdor/jbrowse/data +Bactrocera_oleae|/app/data/other_species/bacole/jbrowse/data +Bemisia_tabaci|/app/data/other_species/bemtab/jbrowse/data +Blattella_germanica|/app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data +Bombus_impatiens|/app/data/other_species/bomimp/BIMP_2.1/jbrowse/data +Bombus_terrestris|/app/data/other_species/bomter/Bter_1.0/jbrowse/data +Bradysia_coprophila|/app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data +Catajapyx_aquilonaris|/app/data/BCM_i5k_pilot/cataqu/jbrowse/data +Centruroides_sculpturatus|/app/data/BCM_i5k_pilot/censcu/jbrowse/data +Cephus_cinctus|/app/data/other_species/cepcin/Ccin1/jbrowse/data/ +Ceratitis_capitata|/app/data/BCM_i5k_pilot/cercap/jbrowse/data +Chelonus_insularis|/app/data/other_species/cheins/ASM1335770v1/jbrowse/data +Cimex_lectularius|/app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data +Clitarchus_hookeri|/app/data/other_species/clihoo/jbrowse/data +Contarinia_nasturtii|/app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data +Copidosoma_floridanum|/app/data/BCM_i5k_pilot/copflo/jbrowse/data +Diabrotica_virgifera_training|/app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data +Diachasma_alloeum|/app/data/other_species/diaall/Dall2.0/jbrowse/data +Diaphorina_citri|/app/data/other_species/diacit/jbrowse/data +Diaphorina_citri_legacy|/app/data/other_species/diacit_legacy/jbrowse/data +Drosophila_biarmipes|/app/data/modencode/drobia/Dbia_2.0/jbrowse/data +Drosophila_bipectinata|/app/data/modencode/drobip/Dbip_2.0/jbrowse/data +Drosophila_elegans|/app/data/modencode/droele/Dele_2.0/jbrowse/data +Drosophila_eugracilis|/app/data/modencode/droeug/Deug_2.0/jbrowse/data +Drosophila_ficusphila|/app/data/modencode/drofic/Dfic_2.0/jbrowse/data +Drosophila_kikkawai|/app/data/modencode/drokik/Dkik_2.0/jbrowse/data +Drosophila_rhopaloa|/app/data/modencode/drorho/Drho_2.0/jbrowse/data +Drosophila_takahashii|/app/data/modencode/drotak/Dtak_2.0/jbrowse/data +Dufourea_novaeangliae|/app/data/other_species/dufnov/jbrowse/data +Ephemera_danica|/app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ +Eufriesea_mexicana|/app/data/other_species/eufmex/ASM148370v1/jbrowse/data +Euglossa_dilemma|/app/data/other_species/eugdil/jbrowse/data +Eurytemora_affinis|/app/data/BCM_i5k_pilot/euraff/jbrowse/data +Eurytemora_affinis_-_training|/app/data/BCM_i5k_pilot/euraff/jbrowse/data +Fopius_arisanus|/app/data/other_species/fopari/jbrowse/data +Frankliniella_occidentalis|/app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data +Galleria_mellonella|/app/data/other_species/galmel/ASM364042v2/jbrowse/data +Gerris_buenoi|/app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ +Habropoda_laboriosa|/app/data/other_species/hablab/jbrowse/data +Halyomorpha_halys|/app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data +Heliothis_virescens|/app/data/other_species/helvir/jbrowse/data/ +Holacanthella_duospinosa|/app/data/other_species/holduo/ASM273828v1/jbrowse/data +Homalodisca_vitripennis|/app/data/BCM_i5k_pilot/homvit/jbrowse/data +Hyalella_azteca|/app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data +Laodelphax_striatellus|/app/data/other_species/laostr/ASM333518v2/jbrowse/data +Lasioglossum_albipes|/app/data/other_species/lasalb/jbrowse/data +Latrodectus_hesperus|/app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data +Leptinotarsa_decemlineata|/app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data +Leptinotarsa_decemlineata_training|/app/data/BCM_i5k_pilot/lepdec/jbrowse/data +Limnephilus_lunatus|/app/data/BCM_i5k_pilot/limlun/jbrowse/data +Locusta_migratoria|/app/data/other_species/locmig/jbrowse/data/ +Loxosceles_reclusa|/app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data +Mamestra_configurata|/app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data +Manduca_sexta|/app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data +Mayetiola_destructor|/app/data/other_species/maydes/jbrowse/data +Medauroidea_extradentata|/app/data/other_species/medext/GCA_003012365.1/jbrowse/data +Megachile_rotundata|/app/data/other_species/megrot/jbrowse/data +Melipona_quadrifasciata|/app/data/other_species/melqua/jbrowse/data +Microplitis_demolitor|/app/data/other_species/micdem/jbrowse/data +Neodiprion_lecontei|/app/data/other_species/neolec/Nlec1.1/jbrowse/data +Neodiprion_lecontei_training|/app/data/other_species/neolec/jbrowse/data +Nicrophorus_vespilloides|/app/data/other_species/nicves/jbrowse/data +Nylanderia_fulva|/app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data +Odontomachus_brunneus|/app/data/other_species/odobru/Obru_v1/jbrowse/data +Oncopeltus_fasciatus|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data +Oncopeltus_fasciatus_training|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data +Onthophagus_taurus|/app/data/BCM_i5k_pilot/onttau/jbrowse/data +Orussus_abietinus|/app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data +Osmia_lignaria|/app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data +Pachypsylla_venusta|/app/data/BCM_i5k_pilot/pacven/jbrowse/data +Parasteatoda_tepidariorum|/app/data/BCM_i5k_pilot/partep/jbrowse/data +Photinus_pyralis|/app/data/other_species/phopyr/Ppyr1.3/jbrowse/data +Rhagoletis_zephyria|/app/data/other_species/rhazep/jbrowse/data +Rhipicephalus_microplus|/app/data/other_species/rhimic/jbrowse/data +Rhyzopertha_dominica|/app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data +Saccharomyceseubayanus|/app/data/other_species/saceub/SEUB3.0/jbrowse/data +Tigriopus_californicus|/app/data/other_species/tigcal/jbrowse/data +Tribolium_castaneum|/app/data/other_species/tricas/jbrowse/data +Trichogramma_pretiosum|/app/data/BCM_i5k_pilot/tripre/jbrowse/data +Varroa_destructor|/app/data/other_species/vardes/Vdes_3.0/jbrowse/data +Varroa_jacobsoni|/app/data/other_species/varjac/vjacob_1.0/jbrowse/data diff --git a/move_back_scripts/stage/organism_list_orig.txt b/move_back_scripts/stage/organism_list_orig.txt new file mode 100644 index 0000000..a9cb8ad --- /dev/null +++ b/move_back_scripts/stage/organism_list_orig.txt @@ -0,0 +1,131 @@ +webapollo_2=# select common_name, directory from organism ORDER by common_name; + common_name | directory +------------------------------------+------------------------------------------------------------- + 10_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 11_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 12_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 13_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 14_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 15_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 16_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 17_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 18_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 19_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 1_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 20_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 21_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 22_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 23_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 24_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 25_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 26_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 27_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 28_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 29_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 2_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 30_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 31_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 32_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 33_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 34_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 35_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 36_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 37_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 38_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 39_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 3_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 40_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 4_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 5_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 6_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 7_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 8_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 9_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + Aethina_tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus_planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois_transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora_glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis_mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia_rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera_cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera_dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera_oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia_tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella_germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus_impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Bombus_terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Catajapyx_aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides_sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus_cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis_capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus_insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex_lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus_hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia_nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma_floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma_alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina_citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina_citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila_biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila_bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila_elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila_eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila_ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila_kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Drosophila_rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila_takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Dufourea_novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera_danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea_mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa_dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora_affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora_affinis_-_training | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius_arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella_occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria_mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris_buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda_laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha_halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis_virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella_duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca_vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella_azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona_fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax_striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum_albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus_hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa_decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Leptinotarsa_decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Limnephilus_lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta_migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles_reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Mamestra_configurata | /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data + Manduca_sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola_destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea_extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile_rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona_quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis_demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion_lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Neodiprion_lecontei_training | /app/data/other_species/neolec/jbrowse/data + Nicrophorus_vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia_fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus_brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus_fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus_fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Onthophagus_taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + Orussus_abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia_lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla_venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda_tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis_zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus_microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha_dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Test organism | /app/data/other_species/aettum/jbrowse/data + Tigriopus_californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium_castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma_pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa_destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Varroa_jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data +(126 rows) + diff --git a/organisms/dev/conf_checksums.md5 b/organisms/dev/conf_checksums.md5 new file mode 100644 index 0000000..b906b79 --- /dev/null +++ b/organisms/dev/conf_checksums.md5 @@ -0,0 +1,126 @@ +9875a5e7cf043a27f48495fab6f8c486 ./10_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./11_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./12_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./13_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./14_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./15_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./16_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./17_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./18_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./19_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./1_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./20_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./21_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./22_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./23_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./24_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./25_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./26_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./27_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./28_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./29_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./2_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./30_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./31_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./32_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./33_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./34_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./35_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./36_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./37_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./38_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./39_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./3_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./40_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./4_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./5_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./6_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./7_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./8_-_Onthophagus_taurus_training/trackList.json +9875a5e7cf043a27f48495fab6f8c486 ./9_-_Onthophagus_taurus_training/trackList.json +73646df96da1166cd30a38bebf80195a ./Aethina_tumida/trackList.json +2a1972b947f6841c9a9aed9e5679476d ./Agrilus_planipennis/trackList.json +74ba054dd52792a38a486216d3e470cb ./Amyelois_transitella/trackList.json +910d3a4c0f0ab1cf0c8806c1e9befcf2 ./Anoplophora_glabripennis/trackList.json +bc6b5a0451bca2cb1441e2d2bbe04910 ./Apis_mellifera/trackList.json +2dc6f71365969d06c76008146329cd46 ./Athalia_rosae/trackList.json +6df1714763887e190e1140bd70c6306a ./Bactrocera_cucurbitae/trackList.json +827fac31d06e3d6d9d2aa507015af66d ./Bactrocera_dorsalis/trackList.json +981ba92d98c51e350171a303174cea72 ./Bactrocera_oleae/trackList.json +459a489feb018e0e59735cf3ae0cb19e ./Bemisia_tabaci/trackList.json +de9fd3c3240021ed7f08e2990953ef12 ./Blattella_germanica/trackList.json +0cfc7188f49a855d833d9f7edc5c4c43 ./Bombus_impatiens/trackList.json +d319d967516ec006c420db1ce685092d ./Bombus_terrestris/trackList.json +63d967caecb7b8b718fb96af5668cf4a ./Catajapyx_aquilonaris/trackList.json +6e0964cd65cab811ae6d66d6c7186175 ./Centruroides_sculpturatus/trackList.json +be0acc687c254929835a118242c8b80d ./Cephus_cinctus/trackList.json +b78fbb636f2dc1bdfea5408d5c9034dc ./Ceratitis_capitata/trackList.json +5cb5a771c75b9795440f1c68b8dbebbe ./Chelonus_insularis/trackList.json +258e614e2f20e1051be0ac4c046ae7d5 ./Cimex_lectularius/trackList.json +9b4647705c606f8cd3a5d826c18e407c ./Clitarchus_hookeri/trackList.json +b319c4301e820bd0c444f7275480615c ./Contarinia_nasturtii/trackList.json +3b1f61d8c934d0a43a5db68f30a62442 ./Copidosoma_floridanum/trackList.json +fcb317d6e0c4ab815449b207a11efe87 ./Diachasma_alloeum/trackList.json +b77db88c5344a3b5ed0886c87ecde93f ./Diaphorina_citri_legacy/trackList.json +ff0d272b2b55ed87b948e4316a61e6b8 ./Diaphorina_citri/trackList.json +9a4ad20f8d07b47bd4ac616732af8f2f ./Drosophila_biarmipes/trackList.json +6e24f24d7dbf6663971b785851762241 ./Drosophila_bipectinata/trackList.json 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./Frankliniella_occidentalis/trackList.json +c235409a662dd7d4e5983d5c55f21f42 ./Galleria_mellonella/trackList.json +f50f8110ff572b3b901f99c181299641 ./Gerris_buenoi/trackList.json +255444ae665abc7679b87dddba3de9b4 ./Habropoda_laboriosa/trackList.json +cea33bcb2db50270eaceb05076b5ce4f ./Halyomorpha_halys/trackList.json +14db59e7b6d54dc08664e6c54f1d39bb ./Heliothis_virescens/trackList.json +e2f52b4118009cf89ea6bfdc501089eb ./Holacanthella_duospinosa/trackList.json +e9bc561ec56b301252f1ffb0c540efef ./Homalodisca_vitripennis/trackList.json +fd3b60db8381052776abf8116fd0180c ./Hyalella_azteca/trackList.json +64520b48d10e0c9e96974fb88646a426 ./Ladona_fulva/trackList.json +854cdac934afc5b82f7ff37cd849170e ./Laodelphax_striatellus/trackList.json +685a1e08f0f029e6545011c582804775 ./Lasioglossum_albipes/trackList.json +2a28cb284299243eb56ee11d714ffa7a ./Latrodectus_hesperus/trackList.json +e84a20706602a27116d3e7f003be96ba ./Leptinotarsa_decemlineata/trackList.json 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./Nicrophorus_vespilloides/trackList.json +d640ee444d670cf6dcc7455e15b6c89f ./Nylanderia_fulva/trackList.json +2a6a62658253a3b5501ca1f8d29a28cf ./Odontomachus_brunneus/trackList.json +2686590197f1bdc037a38fd60e665ee1 ./Oncopeltus_fasciatus/trackList.json +2686590197f1bdc037a38fd60e665ee1 ./Oncopeltus_fasciatus_training/trackList.json +957907b8a69c08037d5ed3db39816f98 ./Onthophagus_taurus/trackList.json +33d35d86dbfc312c8cdba1a5a561a879 ./Orussus_abietinus/trackList.json +35f9a1a800f0572ec5ce46fc6b12790b ./Osmia_lignaria/trackList.json +f81b350db3ea1a82a6d1253d7a0db8fb ./Pachypsylla_venusta/trackList.json +7c458ee03cbe372d5bd8ece05e65fefa ./Parasteatoda_tepidariorum/trackList.json +e71a903e88a05f21faccc3b02f7f67a3 ./Rhagoletis_zephyria/trackList.json +01f29c90f3798a7ceda00cfd97fabeae ./Rhipicephalus_microplus/trackList.json +8eae42f5e10a133030361a0c5a88a754 ./Rhyzopertha_dominica/trackList.json +73646df96da1166cd30a38bebf80195a ./Testorganism/trackList.json 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Arthropoda", + "label" : "protein2genome_Arthropoda", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Cephalochordata", + "label" : "protein2genome_Cephalochordata", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Crustacea", + "label" : "protein2genome_Crustacea", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Cephalochordata", + "label" : "protein2genome_Cephalochordata", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Chelicerata", + "label" : "protein2genome_Chelicerata", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Cnidaria", + "label" : "protein2genome_Cnidaria", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Crustacea", + "label" : "protein2genome_Crustacea", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Mollusca", + "label" : "protein2genome_Mollusca", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Nematomorpha", + "label" : "protein2genome_Nematomorpha", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Parazoa", + "label" : "protein2genome_Parazoa", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Platyhelminthes", + "label" : "protein2genome_Platyhelminthes", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Tardigrada", + "label" : "protein2genome_Tardigrada", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_UNCATEGORISED", + "label" : "protein2genome_UNCATEGORISED", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "snap" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Reference Assembly", + "key" : "Gaps in assembly", + "label" : "Gaps in assembly", + "metadata" : { + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "neg_color" : "white", + "pos_color" : "black" + }, + "type" : "JBrowse/View/Track/Wiggle/Density", + "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "0.5", + "category" : "Reference Assembly", + "key" : "GC Content", + "label" : "GC Content", + "metadata" : { + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Cnidaria", + "label" : "protein2genome_Cnidaria", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Crustacea", + "label" : "protein2genome_Crustacea", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Mollusca", + "label" : "protein2genome_Mollusca", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Nematomorpha", + "label" : "protein2genome_Nematomorpha", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Parazoa", + "label" : "protein2genome_Parazoa", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Platyhelminthes", + "label" : "protein2genome_Platyhelminthes", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Tardigrada", + "label" : "protein2genome_Tardigrada", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_UNCATEGORISED", + "label" : "protein2genome_UNCATEGORISED", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "snap" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Reference Assembly", + "key" : "Gaps in assembly", + "label" : "Gaps in assembly", + "metadata" : { + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "neg_color" : "white", + "pos_color" : "black" + }, + "type" : "JBrowse/View/Track/Wiggle/Density", + "urlTemplate" : "bigwig/onttau_genome.fa.gaps.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "0.5", + "category" : "Reference Assembly", + "key" : "GC Content", + "label" : "GC Content", + "metadata" : { + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "neg_color" : "rgba(255,255,0,50)", + "pos_color" : "rgba(0,0,255,50)" + }, + "type" : "JBrowse/View/Track/Wiggle/Density", + "urlTemplate" : "bigwig/onttau_genome.fa.gc.bigwig" + }, + { + "category" : "Transcriptome/Mapped Reads", + "key" : "Onthophagus taurus early male pupa brain transcripts", + "label" : "Onthophagus taurus early male pupa brain transcripts", + "metadata" : { + "Analysis method" : "tophat2 v2.1.0", + "Date completed" : "Nov-15", + "File provider" : "Eduardo E Zattara, Indiana University Bloomington", + "Geographical location of specimen collection" : "United States, Mapple View Farm, NC", + "NCBI TaxID" : "166361", + "Other methods" : "Trimmomatic 0.32", + "Other notes on methods" : "Part of a larger project still unpublished", + "Other organism notes" : "Large male", + "Publication Status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Cnidaria", + "label" : "protein2genome_Cnidaria", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Crustacea", + "label" : "protein2genome_Crustacea", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Mollusca", + "label" : "protein2genome_Mollusca", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Nematomorpha", + "label" : "protein2genome_Nematomorpha", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Parazoa", + "label" : "protein2genome_Parazoa", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Platyhelminthes", + "label" : "protein2genome_Platyhelminthes", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Tardigrada", + "label" : "protein2genome_Tardigrada", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Mollusca", + "label" : "protein2genome_Mollusca", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Nematomorpha", + "label" : "protein2genome_Nematomorpha", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Parazoa", + "label" : "protein2genome_Parazoa", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Nemata", + "label" : "protein2genome_Nemata", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Green - insertion in the read relative to the reference
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Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "File note" : "This track replaces the previous track, 'Aros_ID06'.", + "Alignment method" : "TopHat 2.0, default parameters", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Data Provider" : "Baylor College of Medicine" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "Aros_ID06", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae female-2 raw reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/Aros_ID07.bam", + "metadata" : { + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/DFED2491-A36F-41E0-BE8B-DDEDAE6050FD/align_summary.txt", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "File note" : "This track replaces the previous track, 'Aros_ID07'.", + "Alignment method" : "TopHat 2.0, default parameters", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Data Provider" : "Baylor College of Medicine" + }, + "label" : "Aros_ID07", + "type" : "WebApollo/View/Track/DraggableAlignments", + "category" : "Transcriptome/Mapped Reads", + "key" : "A. rosae male-2 raw reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/Aros_ID08.bam", + "metadata" : { + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C72E8FAE-2A8F-48CC-8E81-E763757DC126/align_summary.txt", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "File note" : "This track replaces the previous track, 'Aros_ID08'.", + "Alignment method" : "TopHat 2.0, default parameters", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Data Provider" : "Baylor College of Medicine" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "Aros_ID08", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae male-1 raw reads" + }, + { + "style" : { + "neg_color" : "rgba(255,255,0,50)", + "pos_color" : "rgba(0,0,255,50)" + }, + "bicolor_pivot" : "0.5", + "key" : "GC Content", + "scoreType": "avgScore", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Aros01112013-genome_GC.bigwig", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track contact" : "The i5k workspace@NAL" + }, + "type" : "JBrowse/View/Track/Wiggle/Density", + "label" : "GC Content" + }, + { + "style" : { + "neg_color" : "white", + "pos_color" : "black" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "key" : "Gaps in assembly", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Aros01112013-GAPS.bigwig", + "label" : "Gaps in assembly", + "metadata" : { + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track contact" : "The i5k workspace@NAL" + }, + "category" : "Reference Assembly", + "type" : "JBrowse/View/Track/Wiggle/Density" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "A. rosae females-combined Trinity transcriptome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/atro-females-comb_est2genome/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads from two females were concatenated and then assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Assembly", + "label" : "atro-females-comb_est2genome", + "type" : "FeatureTrack" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "A. rosae male-1 Trinity transcriptome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/atro-male-1_est2genome/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Assembly", + "label" : "atro-male-1_est2genome", + "type" : "FeatureTrack" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "A. rosae male-2 Trinity transcriptome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/atro-male-2_est2genome/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Assembly", + "label" : "atro-male-2_est2genome", + "type" : "FeatureTrack" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_male-1_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae male-1 cleaned reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-2_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_male-2_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae male-2 cleaned reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_female-1_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae female-1 cleaned reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 " + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_female-2_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae female-2 cleaned reads" + }, + { + "style" : { + "clip_marker_color" : "red", + "pos_color" : "#FFA600", + "neg_color" : "#005EFF", + "height" : 50 + }, + "bicolor_pivot" : "zero", + "key" : " A. rosae female-1 cleaned reads, XY-plots", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bigwig", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Coverage plots (BigWig)", + "label" : "aros_female-1_tophat-accepted_hits_bigwig" + }, + { + "style" : { + "clip_marker_color" : "red", + "pos_color" : "#FFA600", + "neg_color" : "#005EFF", + "height" : 50 + }, + "bicolor_pivot" : "zero", + "key" : " A. rosae female-2 cleaned reads, XY-plots", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bigwig", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 " + }, + "category" : "Transcriptome/Coverage plots (BigWig)", + "label" : "aros_female-2_tophat-accepted_hits_bigwig" + }, + { + "style" : { + "clip_marker_color" : "red", + "pos_color" : "#FFA600", + "neg_color" : "#005EFF", + "height" : 50 + }, + "bicolor_pivot" : "zero", + "key" : " A. rosae male-1 cleaned reads, XY-plots", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bigwig", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine" + } + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "protein2genome_Tardigrada", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "label" : "protein2genome_Tardigrada", + "type" : "FeatureTrack", + "category" : "BCM_v0.5.3/3. 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At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track contact" : "The i5k workspace@NAL" + } + }, + { + "style" : { + "pos_color" : "#00BFFF", + "neg_color" : "BG_RNAseq_heads_NCSU" + }, + "bicolor_pivot" : "zero", + "key" : "BG_RNAseq_heads_NCSU", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/TopHat2-SE_Lane1_2_Sample3_4_merged-2015-09-01-21-37-00.7/TopHat2-SE_Lane1_2_Sample3_4_merged.bam", + "metadata" : { + "RNA dataset name" : "BG_RNAseq_heads_NCSU", + "Species name" : "Blattella germanica", + "Data Source 3 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/BF73CC50-6318-4461-B672-6C83180CEA43/align_summary.txt", + "Note" : "This is merged dataset from four separate sources", + "Data Source 2 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/C417CB73-E609-49FB-89CC-EEA20455B734/align_summary.txt", + "Data Source 4 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/DAA3D4D7-4D22-451D-9914-EAD37D2E0A5B/align_summary.txt", + "Data Source 1 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/040B27B4-069D-4B29-9F17-851270ED0534/align_summary.txt", + "Data Provider" : "Coby Schal, NCSU" + }, + "type" : "WebApollo/View/Track/DraggableAlignments", + "category" : "Transcriptome/Mapped Reads", + "label" : "BG_RNAseq_heads_NCSU" + }, + { + "style" : { + "neg_color" : "BG_RNAseq_heads_NCSU", + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "key" : "BG_RNAseq_heads_NCSU (Coverage Plot)", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/TopHat2-SE_Lane1_2_Sample3_4_merged-2015-09-01-21-37-00.7/TopHat2-SE_Lane1_2_Sample3_4_merged.bigwig", + "metadata" : { + "RNA dataset name" : "BG_RNAseq_heads_NCSU", + "Species name" : "Blattella germanica", + "Data Source 3 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/BF73CC50-6318-4461-B672-6C83180CEA43/align_summary.txt", + "Note" : "This is merged dataset from four separate sources", + "Data Source 2 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/C417CB73-E609-49FB-89CC-EEA20455B734/align_summary.txt", + "Data Source 4 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/DAA3D4D7-4D22-451D-9914-EAD37D2E0A5B/align_summary.txt", + "Data Source 1 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/040B27B4-069D-4B29-9F17-851270ED0534/align_summary.txt", + "Data Provider" : "Coby Schal, NCSU" + }, + "label" : "BG_RNAseq_heads_NCSU (Coverage Plot)", + "category" : "Transcriptome/Coverage Plots (BigWig)", + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/SRR1552487_SRR1552488_merged-2015-09-01-18-15-30.1/SRR1552487_SRR1552488_merged.bam", + "label" : "BG_RNAseq_heads_UW", + "type" : "WebApollo/View/Track/DraggableAlignments", + "category" : "Transcriptome/Mapped Reads", + "metadata" : { + "Data URL" : "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488", + "Alignment summary" : "PE_SRR1552487: http://de.iplantcollaborative.org/dl/d/C663364F-AAA3-427F-8DFD-27772ED2BDCB/align_summary.txt; PE_SRR1552488: http://de.iplantcollaborative.org/dl/d/908426A6-7915-4CB4-9EA7-ABDA19590C4F/align_summary.txt", + "Other notes" : "tophat parameters: PE_SRR1552487: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552487_read1.fastq' --file_query2 'SRR1552487_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'; PE_SRR1552488: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552488_read1.fastq' --file_query2 'SRR1552488_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'", + "Citation" : "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700", + "File provider" : "Kim Walden, UIUC", + "Data provider" : "Inez Anna Drinnenberg", + "Track legend" : "Reads from SRR1552487 and SRR1552488 were aligned to the B. germanica assembly in TopHat, and the resulting alignment files were merged. Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "key" : "BG_RNAseq_heads_UW" + }, + { + "style" : { + "pos_color" : "#00BFFF", + "neg_color" : "BG_RNAseq_heads_UW" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "key" : "BG_RNAseq_heads_UW (Coverage Plot)", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/SRR1552487_SRR1552488_merged-2015-09-01-18-15-30.1/SRR1552487_SRR1552488_merged-nosecondary.bigwig", + "metadata" : { + "Data URL" : "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488", + "Other notes" : "tophat parameters: PE_SRR1552487: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552487_read1.fastq' --file_query2 'SRR1552487_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'; PE_SRR1552488: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552488_read1.fastq' --file_query2 'SRR1552488_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'", + "Alignment summary" : "PE_SRR1552487: http://de.iplantcollaborative.org/dl/d/C663364F-AAA3-427F-8DFD-27772ED2BDCB/align_summary.txt; PE_SRR1552488: http://de.iplantcollaborative.org/dl/d/908426A6-7915-4CB4-9EA7-ABDA19590C4F/align_summary.txt", + "File provider" : "Kim Walden, UIUC", + "Citation" : "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700", + "Data provider" : "Inez Anna Drinnenberg", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage. 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Lauderdale conditions of data re-use." + }, + "key" : "blastx_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Transcriptome of the egg parasitoid Fopius arisanus: an important biocontrol tool for Tephritid fruit fly suppression, Gigascience, 2015, 4:36 doi:10.1186/s13742-015-0075-4 (http://www.gigasciencejournal.com/content/4/1/36)", + "File provider":"Scott Geib, USDA-ARS-PBARC", + "Analysis method":"TopHat v2.0.13", + "Date completed":"12/2/15" +}, + "label" : "Fari_RNAseq_female (Coverage Plot)", + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "style" : { + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "key" : "Fari_RNAseq_male (Coverage Plot)", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "user_contributed_data/sgeib/Fari_i5k/male_accepted_hits_refSeq_IDs.bigwig", + +"category" : "Transcriptome/Coverage Plots (BigWig)", +"metadata" : { + "Geographical location of specimen collection":"Fari Lab colony Bdor adapted, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI", + "Tissues included":"Pooled Adult Male ", + "Sex ":"Male", + "Strain":"Fari_Bdor", + "Other notes":"See publication and NCBI Bioproject for sample details", + "NCBI SRA accession #":"SRA: SRX689037", + "Sequencing platform and version":"Illumina HiSeq2000, 2x100 bp PE", + "Data source URL":"http://www.ncbi.nlm.nih.gov/bioproject/259572", + "Publication status":"Published. Calla et al. Transcriptome of the egg parasitoid Fopius arisanus: an important biocontrol tool for Tephritid fruit fly suppression, Gigascience, 2015, 4:36 doi:10.1186/s13742-015-0075-4 (http://www.gigasciencejournal.com/content/4/1/36)", + "File provider":"Scott Geib, USDA-ARS-PBARC", + "Analysis method":"TopHat v2.0.13", + "Date completed":"12/2/15" +}, + "label" : "Fari_RNAseq_male (Coverage Plot)", + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "style" : { + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "key" : "Fari_RNAseq_larvae (Coverage Plot)", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "user_contributed_data/sgeib/Fari_i5k/larvae_accepted_hits_refSeq_IDs.bigwig", + +"category" : "Transcriptome/Coverage Plots (BigWig)", +"metadata" : { + "Geographical location of specimen collection":"Fari Lab colony Bdor adapted, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI", + "Tissues included":"Pooled Larvae", + "Sex ":"Pool", + "Strain":"Fari_Bdor", + "Other notes":"See publication and NCBI Bioproject for sample details", + "NCBI SRA accession #":"SRA: SRX689040", + "Sequencing platform and version":"Illumina HiSeq2000, 2x100 bp PE", + "Data source URL":"http://www.ncbi.nlm.nih.gov/bioproject/259570", + "Publication status":"Published. Calla et al. Transcriptome of the egg parasitoid Fopius arisanus: an important biocontrol tool for Tephritid fruit fly suppression, Gigascience, 2015, 4:36 doi:10.1186/s13742-015-0075-4 (http://www.gigasciencejournal.com/content/4/1/36)", + "File provider":"Scott Geib, USDA-ARS-PBARC", + "Analysis method":"TopHat v2.0.13", + "Date completed":"12/2/15" +}, + "label" : "Fari_RNAseq_larvae (Coverage Plot)", + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "user_contributed_data/sgeib/Fari_i5k/pupae_accepted_hits_refSeq_IDs.bigwig", + +"category" : "Transcriptome/Coverage Plots (BigWig)", +"metadata" : { + "Geographical location of specimen collection":"Fari Lab colony Bdor adapted, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI", + "Tissues included":"Pooled Pupae", + "Sex ":"Pool", + "Strain":"Fari_Bdor", + "Other notes":"See publication and NCBI Bioproject for sample details", + "NCBI SRA accession #":"SRA: SRX689038", + "Sequencing platform and version":"Illumina HiSeq2000, 2x100 bp PE", + "Data source URL":"http://www.ncbi.nlm.nih.gov/bioproject/259571", + "Publication status":"Published. Calla et al. Transcriptome of the egg parasitoid Fopius arisanus: an important biocontrol tool for Tephritid fruit fly suppression, Gigascience, 2015, 4:36 doi:10.1186/s13742-015-0075-4 (http://www.gigasciencejournal.com/content/4/1/36)", + "File provider":"Scott Geib, USDA-ARS-PBARC", + "Analysis method":"TopHat v2.0.13", + "Date completed":"12/2/15" +}, + "style" : { + "pos_color" : "#00BFFF" + }, + "label" : "Fari_RNAseq_pupae (Coverage Plot)", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "bicolor_pivot" : "zero", + "key" : "Fari_RNAseq_pupae (Coverage Plot)", + "autoscale" : "local" + } + ], + "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico", + "alwaysOnTracks" : "DNA,Annotations", + "formatVersion" : 1 +} diff --git a/organisms/stage/Frankliniella_occidentalis/trackList.json b/organisms/stage/Frankliniella_occidentalis/trackList.json new file mode 100644 index 0000000..bf5ef5e --- /dev/null +++ b/organisms/stage/Frankliniella_occidentalis/trackList.json @@ -0,0 +1,232 @@ +{ + "formatVersion" : 1, + "names" : { + "type" : "Hash", + "url" : "names/" + }, + "tracks" : [ + { + "category" : "Reference sequence", + "chunkSize" : 20000, + "key" : "Reference sequence", + "label" : "DNA", + "seqType" : "dna", + "storeClass" : "JBrowse/Store/Sequence/StaticChunked", + "type" : "SequenceTrack", + "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Reference Assembly", + "key" : "Gaps in assembly", + "label" : "Gaps in assembly", + "metadata" : { + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of gaps in the reference assembly. 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Green - insertion in the read relative to the reference
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Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "est2genome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "category" : "BCM_v0.5.3/3. Mapped DNA/Other", + "urlTemplate" : "tracks/est2genome/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est2genome" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Source data" : "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955374/SRR955374.sra", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "alignment summary" : "http://de.iplantcollaborative.org/dl/d/25F3B191-FD45-481F-B236-022EC0B20089/align_summary.txt" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_larvae_accepted_hits_refSeq_IDs.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "RNA-Seq/Coverage Plots (BigWig)", + "key" : "Microplitis demolitor venom_gland (Coverage Plot)", + "label" : "Microplitis demolitor venom_gland (Coverage Plot)", + "metadata" : { + "Analysis method" : "Tophat v2.0.9", + "Analysis parameters" : "--align_reads 'together' --mate-inner-dist '50' --file_query 'SRR955397_1.fastq' --file_query2 'SRR955397_2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database '69319_ref_Mdem2_chrUn.fa' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'", + "Data provider" : "Gaelen Burke and Mike Strand, University of Georgia", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Source data" : "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955397/SRR955397.sra", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "alignment summary" : "http://de.iplantcollaborative.org/dl/d/7A0402D9-53BA-4ACF-8D71-F74BAAF3DF2B/align_summary.txt" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_venom_gland_accepted_hits_refSeq_IDs.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "RNA-Seq/Coverage Plots (BigWig)", + "key" : "Microplitis demolitor teratocytes (Coverage Plot)", + "label" : "Microplitis demolitor teratocytes (Coverage Plot)", + "metadata" : { + "Analysis method" : "Tophat v2.0.9", + "Analysis parameters" : "--align_reads 'together' --mate-inner-dist '50' --file_query 'SRR955076.sra_1.fastq' --file_query2 'SRR955076.sra_2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database '69319_ref_Mdem2_chrUn.fa' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'", + "Data provider" : "Gaelen Burke and Mike Strand, University of Georgia", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Source data" : "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955076/SRR955076.sra", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "alignment summary" : "http://de.iplantcollaborative.org/dl/d/0AD340BA-F2AC-4E60-BCD3-7082201ED087/align_summary.txt" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_teratocytes_accepted_hits_refSeq_IDs.bigwig" + }, + { + "category" : "Mapped DNA/Microplitis demolitor ovary DNA", + "key" : "Microplitis demolitor ovary DNA, mapped reads", + "label" : "Microplitis demolitor ovary DNA, mapped reads", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739298/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420507", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1128/JVI.01388-15", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/3t4wo_sort.bam" + }, + { + "category" : "Mapped DNA/Microplitis demolitor bracovirus DNA", + "key" : "Microplitis demolitor bracovirus DNA, mapped reads", + "label" : "Microplitis demolitor bracovirus DNA, mapped reads", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739297/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420508", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/mdbv_all_sort.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Microplitis demolitor ovary DNA", + "key" : "Microplitis demolitor ovary DNA (Coverage Plot)", + "label" : "Microplitis demolitor ovary DNA (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739298/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420507", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1128/JVI.01388-15", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/3t4wo_sort.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Microplitis demolitor bracovirus DNA", + "key" : "Microplitis demolitor bracovirus DNA (Coverage Plot)", + "label" : "Microplitis demolitor bracovirus DNA (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739297/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420508", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/mdbv_all_sort.bigwig" + }, + { + "category" : "Mapped DNA/Mapped Reads", + "key" : "Infected Chrysodeixis includens hemocytes", + "label" : "Infected Chrysodeixis includens hemocytes", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739316/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRX1047183/", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_hemo_sort_mdbv.bam" + }, + { + "category" : "Mapped DNA/Mapped Reads", + "key" : "Infected Chrysodeixis includens", + "label" : "Infected Chrysodeixis includens", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739318", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766325,SRX3766326,SRX3766328,SRX3766330,SRX3766333,SRX3766334", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_sort_mdbv.bam" + }, + { + "category" : "Mapped DNA/Mapped Reads", + "key" : "Infected Trichoplusia ni", + "label" : "Infected Trichoplusia ni", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739317/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766323,SRX3766324,SRX3766327,SRX3766329,SRX3766331,SRX3766332", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/t_sort_mdbv.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Coverage Plots (BigWig)", + "key" : "Infected Chrysodeixis includens hemocytes (Coverage Plot)", + "label" : "Infected Chrysodeixis includens hemocytes (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739316/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRX1047183/", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_hemo_sort_mdbv.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Coverage Plots (BigWig)", + "key" : "Infected Chrysodeixis includens (Coverage Plot)", + "label" : "Infected Chrysodeixis includens (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739318", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766325,SRX3766326,SRX3766328,SRX3766330,SRX3766333,SRX3766334", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_sort_mdbv.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Coverage Plots (BigWig)", + "key" : "Infected Trichoplusia ni (Coverage Plot)", + "label" : "Infected Trichoplusia ni (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739317", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766323,SRX3766324,SRX3766327,SRX3766329,SRX3766331,SRX3766332", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/t_sort_mdbv.bigwig" + }, + { + "category" : "Mapped DNA/Microplitis demolitor ovary DNA", + "key" : "Microplitis demolitor ovary DNA, mapped reads (1% coverage)", + "label" : "Microplitis demolitor ovary DNA, mapped reads (1% coverage)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739298/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420507", + "Method" : "bwa 0.7.15; Coverage reduced to 1% with GATK", + "Publication status" : "Published - please cite 10.1128/JVI.01388-15", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/3t4wo_sort.RG.Reordered.RCfrac.bam" + }, + { + "category" : "Mapped DNA/Microplitis demolitor bracovirus DNA", + "key" : "Microplitis demolitor bracovirus DNA, mapped reads (0.1% coverage)", + "label" : "Microplitis demolitor bracovirus DNA, mapped reads (0.1% coverage)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739297/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420508", + "Method" : "bwa 0.7.15; Coverage reduced to 0.1% with GATK", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
Yellow marking - mismatch (hover over the mismatch to see what the snp is)" + }, + "label" : "Egg", + "category" : "RNA-Seq/Mapped Reads", + "key" : "Egg" + }, + { + "style" : { + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "key" : "Egg, coverage", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_egg_2nd_passAligned.sortedByCoord.out.bigwig", + "category" : "RNA-Seq/Coverage Plots", + "label" : "Egg, coverage", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984010, SRR6984024, SRR6984030", + "development stage" : "Egg", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_RAW_2nd_passAligned.sortedByCoord.out.bam", + "type" : "WebApollo/View/Track/DraggableAlignments", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984022, SRR6984034, SRR6984031", + "development stage" : "Reproductive Adult Worker", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand
Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
Yellow marking - mismatch (hover over the mismatch to see what the snp is)" + }, + "label" : "Reproductive Adult Worker", + "category" : "RNA-Seq/Mapped Reads", + "key" : "Reproductive Adult Worker" + }, + { + "style" : { + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "key" : "Reproductive Adult Worker, coverage", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_RAW_2nd_passAligned.sortedByCoord.out.bigwig", + "category" : "RNA-Seq/Coverage Plots", + "label" : "Reproductive Adult Worker, coverage", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984022, SRR6984034, SRR6984031", + "development stage" : "Reproductive Adult Worker", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_NRW_2nd_passAligned.sortedByCoord.out.bam", + "type" : "WebApollo/View/Track/DraggableAlignments", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984021, SRR6984013, SRR6984057", + "development stage" : "Non-reproductive Adult Worker", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand
Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
Yellow marking - mismatch (hover over the mismatch to see what the snp is)" + }, + "label" : "Non-reproductive Adult Worker", + "category" : "RNA-Seq/Mapped Reads", + "key" : "Non-reproductive Adult Worker" + }, + { + "style" : { + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "key" : "Non-reproductive Adult Worker, coverage", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_NRW_2nd_passAligned.sortedByCoord.out.bigwig", + "category" : "RNA-Seq/Coverage Plots", + "label" : "Non-reproductive Adult Worker, coverage", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984021, SRR6984013, SRR6984057", + "development stage" : "Non-reproductive Adult Worker", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_queen_2nd_passAligned.sortedByCoord.out.bam", + "type" : "WebApollo/View/Track/DraggableAlignments", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984023, SRR6984033, SRR6984032", + "development stage" : "Queen", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand
Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
Yellow marking - mismatch (hover over the mismatch to see what the snp is)" + }, + "label" : "Queen", + "category" : "RNA-Seq/Mapped Reads", + "key" : "Queen" + }, + { + "style" : { + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "key" : "Queen, coverage", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_queen_2nd_passAligned.sortedByCoord.out.bigwig", + "category" : "RNA-Seq/Coverage Plots", + "label" : "Queen, coverage", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984023, SRR6984033, SRR6984032", + "development stage" : "Queen", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_pupa_2nd_passAligned.sortedByCoord.out.bam", + "type" : "WebApollo/View/Track/DraggableAlignments", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10).The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984020", + "development stage" : "Pupa", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand
Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
Yellow marking - mismatch (hover over the mismatch to see what the snp is)" + }, + "label" : "Pupa", + "category" : "RNA-Seq/Mapped Reads", + "key" : "Pupa" + }, + { + "style" : { + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "key" : "Pupa, coverage", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "analyses/Odontomachus-brunneus-RNA-Seq_2020-06-09_v1.0/Odontomachus_pupa_2nd_passAligned.sortedByCoord.out.bigwig", + "category" : "RNA-Seq/Coverage Plots", + "label" : "Pupa, coverage", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984020", + "development stage" : "Pupa", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "style" : { + "className" : "container-16px", + "subfeatureClasses" : { + "intron" : null, + "stop_codon" : null, + "match_part" : "darkblue-80pct", + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "junction-cds", + "start_codon" : null, + "UTR" : "webapollo-UTR" + }, + "arrowheadClass" : "trellis-arrowhead" + }, + "key" : "Larva, junction reads", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/Larva, junction reads/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "category" : "RNA-Seq/Splice junctions", + "label" : "Larva, junction reads", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale re-use guidelines", + "Data source" : "SRR6984019, SRR6984036, SRR6984027", + "development stage" : "Larva", + "Analysis provider" : "Kim Walden, University of Illinois at Urbana-Champaign", + "Track legend" : "Junction reads" + } + }, + { + "style" : { + "className" : "container-16px", + "subfeatureClasses" : { + "intron" : null, + "stop_codon" : null, + "match_part" : "darkblue-80pct", + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "junction-cds", + "start_codon" : null, + "UTR" : "webapollo-UTR" + }, + "arrowheadClass" : "trellis-arrowhead" + }, + "key" : "Non-reproductive Adult Worker, junction reads", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/Non-reproductive Adult Worker, junction reads/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "category" : "RNA-Seq/Splice junctions", + "label" : "Non-reproductive Adult Worker, junction reads", + "metadata" : { + "Analysis method" : "Reads were trimmed with Trimmomatic (0.32) and aligned to the genome assembly by caste/life-stage using STAR (2.7.3a) in paired-end mode with the available NCBI genome gtf file. The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. 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The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. 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The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. 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The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. 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The reads were aligned to the genome in a second pass using all the available splice junction information from the first pass alignments. Bam files were indexed with SAMtools (1.10). The second pass splice junction output files were converted to bed files using the custom script available at: https://gist.github.com/fabiolib/ffb21853e3eb3780150074aeffc54901", + "Publication status" : "Unpublished - please follow Toronto/Ft. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Platyhelminthes", + "label" : "protein2genome_Platyhelminthes", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Tardigrada", + "label" : "protein2genome_Tardigrada", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_UNCATEGORISED", + "label" : "protein2genome_UNCATEGORISED", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/2. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "snap" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "pooled RNA-seq - cleaned reads", + "label" : "pooled_RNA-seq_cleaned_reads", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "bam/ivargas/cleaned_reads/accepted_hits.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "RNA-Seq/Coverage Plots", + "key" : "pooled RNA-seq - cleaned reads, XY-plot", + "label" : "pooled RNA-seq - cleaned reads, XY-plot", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "clip_marker_color" : "red", + "height" : 50, + "neg_color" : "#005EFF", + "pos_color" : "#FFA600" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "bam/ivargas/cleaned_reads/accepted_hits.bigwig" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "pooled RNA-seq - raw reads", + "label" : "pooled_RNA-seq_raw_reads", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/653A7172-438A-4688-811C-FA92A8FD22E6/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "bam/ivargas/raw_reads/accepted_hits.bam" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "RNA-seq raw PE reads Andolfatto et al.", + "label" : "RNA-seq_Andolfatto_raw_PE_reads", + "metadata" : { + "Alignment method" : "--align_reads together --mate-inner-dist 50 --file_query Oncopeltus_fasciatus_PE_1.fq.gz --file_query2 Oncopeltus_fasciatus_PE_2.fq.gz --library-type fr-unstranded --min-anchor-length 8 --splice-mismatches 0 --min-intron-length 70 --max-intron-length 50000 --min-isoform-fraction 0.15 --max-multihits 20 --min-segment-intron 50 --max-segment-intron 500000 --segment-mismatches 2 --segment-length 20 --num-threads 6 --user_database Ofas.scaffolds.fa --b2-sensitive --tophat_version 2.0.9 --bowtie_version 2.1.0", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/5671A470-68E8-4FF2-AA8F-B55A8CC74AFF/align_summary.txt", + "Data Source" : "http://genomics-pubs.princeton.edu/insect_genomics/data/Oncopeltus_fasciatus.tar", + "Read cleaning method" : "None", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "bam/ivargas/andolfatto_raw_reads/accepted_hits.bam" + }, + { + "autoscale" : "local", + "category" : "RNA-Seq/Coverage Plots", + "key" : "RNA-seq raw PE reads Andolfatto et al, XY-plot", + "label" : "RNA-seq raw PE reads Andolfatto et al, XY-plot", + "metadata" : { + "Alignment method" : "--align_reads together --mate-inner-dist 50 --file_query Oncopeltus_fasciatus_PE_1.fq.gz --file_query2 Oncopeltus_fasciatus_PE_2.fq.gz --library-type fr-unstranded --min-anchor-length 8 --splice-mismatches 0 --min-intron-length 70 --max-intron-length 50000 --min-isoform-fraction 0.15 --max-multihits 20 --min-segment-intron 50 --max-segment-intron 500000 --segment-mismatches 2 --segment-length 20 --num-threads 6 --user_database Ofas.scaffolds.fa --b2-sensitive --tophat_version 2.0.9 --bowtie_version 2.1.0", + "Data Source" : "http://genomics-pubs.princeton.edu/insect_genomics/data/Oncopeltus_fasciatus.tar", + "Read cleaning method" : "None", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip." + }, + "min_score" : 0, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "clip_marker_color" : "red", + "height" : 50, + "neg_color" : "#005EFF", + "pos_color" : "#FFA600" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "bam/ivargas/andolfatto_raw_reads/accepted_hits.bigwig", + "variance_band" : false + }, + { + "category" : "RNA-Seq/Assembly", + "compress" : 0, + "key" : "Maternal and early embryonic 454 transcriptome", + "label" : "mat_embr_454_transcriptome", + "metadata" : { + "Alignment contact" : "Iris Vargas-Jentzsch, University of Cologne", + "Alignment program and Parameters" : "GMAP version 2014-05-15 called with args: Ofas_454.transcriptome_complete_short.fasta -d Ofas.scaffolds -f 2", + "BioProject" : "PRJNA79671; Accession #s SRX022011, SRX022012, SRX022013, SRX022014", + "Data Source" : "http://www.extavourlab.com/resources/Oncopeltus_454transcriptome_BLASTnames_01_2011.fasta
Here we used the complete transcriptome dataset, including singletons, obtained directly from Ben Ewen-Campen (bewencampen at oeb dot harvard dot edu).", + "PMCID" : "PMC3040728", + "PMID" : "21266083", + "Reference" : "Ewen-Campen B., Shaner N., Panfilio K. A., Suzuki Y., Roth S., and Extavour C. G. (2011). The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 12: 61." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "trellis-arrowhead", + "className" : "container-16px", + "subfeatureClasses" : { + "CDS" : "transcriptome-cds", + "UTR" : "transcriptome-utr", + "exon" : "container-100pct", + "wholeCDS" : null + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/mat_embr_454_transcriptome/{refseq}/trackData.json" + }, + { + "category" : "RNA-Seq/Assembly", + "compress" : 0, + "key" : "Benoit Trinity transcriptome", + "label" : "BenoitTrinity_gmapOfas", + "metadata" : { + "Alignment contact" : "Iris Vargas-Jentzsch, University of Cologne", + "Data Source" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/", + "Program and Parameters" : "RNA-Seq: Trinity for assembly and TransDecoder to filter out ORFs.
Mapping to genome: GMAP version 2014-05-15 called with args:
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Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Cnidaria", + "label" : "protein2genome_Cnidaria", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Crustacea", + "label" : "protein2genome_Crustacea", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Parazoa", + "label" : "protein2genome_Parazoa", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Platyhelminthes", + "label" : "protein2genome_Platyhelminthes", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "snap" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "pooled RNA-seq - cleaned reads", + "label" : "pooled_RNA-seq_cleaned_reads", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "bam/ivargas/andolfatto_raw_reads/accepted_hits.bam" + }, + { + "autoscale" : "local", + "category" : "RNA-Seq/Coverage Plots", + "key" : "RNA-seq raw PE reads Andolfatto et al, XY-plot", + "label" : "RNA-seq raw PE reads Andolfatto et al, XY-plot", + "metadata" : { + "Alignment method" : "--align_reads together --mate-inner-dist 50 --file_query Oncopeltus_fasciatus_PE_1.fq.gz --file_query2 Oncopeltus_fasciatus_PE_2.fq.gz --library-type fr-unstranded --min-anchor-length 8 --splice-mismatches 0 --min-intron-length 70 --max-intron-length 50000 --min-isoform-fraction 0.15 --max-multihits 20 --min-segment-intron 50 --max-segment-intron 500000 --segment-mismatches 2 --segment-length 20 --num-threads 6 --user_database Ofas.scaffolds.fa --b2-sensitive --tophat_version 2.0.9 --bowtie_version 2.1.0", + "Data Source" : "http://genomics-pubs.princeton.edu/insect_genomics/data/Oncopeltus_fasciatus.tar", + "Read cleaning method" : "None", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip." + }, + "min_score" : 0, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "clip_marker_color" : "red", + "height" : 50, + "neg_color" : "#005EFF", + "pos_color" : "#FFA600" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "bam/ivargas/andolfatto_raw_reads/accepted_hits.bigwig", + "variance_band" : false + }, + { + "category" : "RNA-Seq/Assembly", + "compress" : 0, + "key" : "Maternal and early embryonic 454 transcriptome", + "label" : "mat_embr_454_transcriptome", + "metadata" : { + "Alignment contact" : "Iris Vargas-Jentzsch, University of Cologne", + "Alignment program and Parameters" : "GMAP version 2014-05-15 called with args: Ofas_454.transcriptome_complete_short.fasta -d Ofas.scaffolds -f 2", + "BioProject" : "PRJNA79671; Accession #s SRX022011, SRX022012, SRX022013, SRX022014", + "Data Source" : "http://www.extavourlab.com/resources/Oncopeltus_454transcriptome_BLASTnames_01_2011.fasta
Here we used the complete transcriptome dataset, including singletons, obtained directly from Ben Ewen-Campen (bewencampen at oeb dot harvard dot edu).", + "PMCID" : "PMC3040728", + "PMID" : "21266083", + "Reference" : "Ewen-Campen B., Shaner N., Panfilio K. A., Suzuki Y., Roth S., and Extavour C. G. (2011). The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 12: 61." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "trellis-arrowhead", + "className" : "container-16px", + "subfeatureClasses" : { + "CDS" : "transcriptome-cds", + "UTR" : "transcriptome-utr", + "exon" : "container-100pct", + "wholeCDS" : null + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/mat_embr_454_transcriptome/{refseq}/trackData.json" + }, + { + "category" : "RNA-Seq/Assembly", + "compress" : 0, + "key" : "Benoit Trinity transcriptome", + "label" : "BenoitTrinity_gmapOfas", + "metadata" : { + "Alignment contact" : "Iris Vargas-Jentzsch, University of Cologne", + "Data Source" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/", + "Program and Parameters" : "RNA-Seq: Trinity for assembly and TransDecoder to filter out ORFs.
Mapping to genome: GMAP version 2014-05-15 called with args:
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Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Green - insertion in the read relative to the reference
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Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est-gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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The score at any position may be seen by moving the cursor to that position in the track.", + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", +}, + "key" : "GC Content", + "scoreType": "avgScore", + + + "autoscale" : "local" + } + ], + "plugins" : [ + { + "location" : "./plugins/WebApollo", + "name" : "WebApollo" + } + ], + "names" : { + "url" : "names/", + "type" : "Hash" + }, + "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico", + "formatVersion" : 1, + "alwaysOnTracks" : "DNA,Annotations" +} diff --git a/organisms/stage/Photinus_pyralis/trackList.json b/organisms/stage/Photinus_pyralis/trackList.json new file mode 100644 index 0000000..ce35688 --- /dev/null +++ b/organisms/stage/Photinus_pyralis/trackList.json @@ -0,0 +1,337 @@ +{ + "formatVersion" : 1, + "names" : { + "type" : "Hash", + "url" : "names/" + }, + "tracks" : [ + { + "category" : "Reference sequence", + "chunkSize" : 20000, + "key" : "Reference sequence", + "label" : "DNA", + "seqType" : "dna", + "storeClass" : "JBrowse/Store/Sequence/StaticChunked", + "type" : "SequenceTrack", + "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Reference Assembly", + "key" : "Gaps in assembly", + "label" : "Gaps in assembly", + "metadata" : { + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of gaps in the reference assembly. 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Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
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Green marking - insertion in the read relative to the reference
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Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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./Ceratitis_capitata/trackList.json +5cb5a771c75b9795440f1c68b8dbebbe ./Chelonus_insularis/trackList.json +258e614e2f20e1051be0ac4c046ae7d5 ./Cimex_lectularius/trackList.json +9b4647705c606f8cd3a5d826c18e407c ./Clitarchus_hookeri/trackList.json +b319c4301e820bd0c444f7275480615c ./Contarinia_nasturtii/trackList.json +4dde816d5c51b79a20b751f9af1295b5 ./Copidosoma_floridanum/trackList.json +49f02a414ec131186d8bfe16aafba07f ./Diabrotica_virgifera_training/trackList.json +44192d73bd17b07c4d96ebb5cf6ce87e ./Diachasma_alloeum/trackList.json +b77db88c5344a3b5ed0886c87ecde93f ./Diaphorina_citri_legacy/trackList.json +ff0d272b2b55ed87b948e4316a61e6b8 ./Diaphorina_citri/trackList.json +9a4ad20f8d07b47bd4ac616732af8f2f ./Drosophila_biarmipes/trackList.json +6e24f24d7dbf6663971b785851762241 ./Drosophila_bipectinata/trackList.json +f2a43993463d5371b924ad02820eda17 ./Drosophila_elegans/trackList.json +9d8b5ace901eb50baf5c5f4d5e8de290 ./Drosophila_eugracilis/trackList.json +0d57c7f0c604348da80f52784ef5302f ./Drosophila_ficusphila/trackList.json +5797c8a7a4336a569d9bbc44aafd9069 ./Drosophila_kikkawai/trackList.json +6f35b7b4701d4deccf60e81d8e8af9f6 ./Drosophila_rhopaloa/trackList.json +9f26a329f6b15adcc0bf081de7430a37 ./Drosophila_takahashii/trackList.json +f8f06ac07efa32fc80cd1c8c762323c6 ./Dufourea_novaeangliae/trackList.json +20859b8e2a368fee17ab67308ba2b7dc ./Ephemera_danica/trackList.json +074a645adae3937b35c8aa350bbc17c9 ./Eufriesea_mexicana/trackList.json +02590ee8edb81a40567c0b86178cb7b9 ./Euglossa_dilemma/trackList.json +1d6fd304321335a046145aa077acc38a ./Eurytemora_affinis/trackList.json +1d6fd304321335a046145aa077acc38a ./Eurytemora_affinis_-_training/trackList.json +9a6963cad06a6cd07d27cf7c428d5c65 ./Fopius_arisanus/trackList.json +c6dca7739768478dbdd6df20daba2fbd ./Frankliniella_occidentalis/trackList.json +c235409a662dd7d4e5983d5c55f21f42 ./Galleria_mellonella/trackList.json +f50f8110ff572b3b901f99c181299641 ./Gerris_buenoi/trackList.json +255444ae665abc7679b87dddba3de9b4 ./Habropoda_laboriosa/trackList.json +cea33bcb2db50270eaceb05076b5ce4f ./Halyomorpha_halys/trackList.json +14db59e7b6d54dc08664e6c54f1d39bb ./Heliothis_virescens/trackList.json +e2f52b4118009cf89ea6bfdc501089eb ./Holacanthella_duospinosa/trackList.json +e9bc561ec56b301252f1ffb0c540efef ./Homalodisca_vitripennis/trackList.json +fd3b60db8381052776abf8116fd0180c ./Hyalella_azteca/trackList.json +854cdac934afc5b82f7ff37cd849170e ./Laodelphax_striatellus/trackList.json +685a1e08f0f029e6545011c582804775 ./Lasioglossum_albipes/trackList.json +2a28cb284299243eb56ee11d714ffa7a ./Latrodectus_hesperus/trackList.json +e84a20706602a27116d3e7f003be96ba ./Leptinotarsa_decemlineata/trackList.json +69a5a4f0e26fec12aaef1eb27488b72f ./Leptinotarsa_decemlineata_training/trackList.json +1a7809c807541f40a6d0de2f1c6b4e7d ./Limnephilus_lunatus/trackList.json +81601f35a3616b5cd0132ec1b3098110 ./Locusta_migratoria/trackList.json +6bee3f4c5af461a730cdcc90da4ffeb7 ./Loxosceles_reclusa/trackList.json +b472bc7087756090613a9a369fd435fb ./Mamestra_configurata/trackList.json +8ff5b2b9c657429aea0280fc6f5fc76c ./Manduca_sexta/trackList.json +67a592e3a7c6b702b0dcc9b9e6771515 ./Mayetiola_destructor/trackList.json +38b7867ca690867f5739962d433c0828 ./Medauroidea_extradentata/trackList.json +9fa0226e20b1e5578a15726c6bc4a238 ./Megachile_rotundata/trackList.json +79cab08b89326d6727dc68e91cb085d6 ./Melipona_quadrifasciata/trackList.json +bdb5bafc32a74022dea3f90d07f03f61 ./Microplitis_demolitor/trackList.json +965665c71fb3f9b549c0af88b012c03b ./Neodiprion_lecontei/trackList.json +d1341c414d452723f630eaf7ae66a2aa ./Neodiprion_lecontei_training/trackList.json +d73b899e0fdfc0b20a1f6c368dc7aac6 ./Nicrophorus_vespilloides/trackList.json +d640ee444d670cf6dcc7455e15b6c89f ./Nylanderia_fulva/trackList.json +0bb2f28b9870d041d0effa2e36ed6214 ./Odontomachus_brunneus/trackList.json +2686590197f1bdc037a38fd60e665ee1 ./Oncopeltus_fasciatus/trackList.json +2686590197f1bdc037a38fd60e665ee1 ./Oncopeltus_fasciatus_training/trackList.json +957907b8a69c08037d5ed3db39816f98 ./Onthophagus_taurus/trackList.json +33d35d86dbfc312c8cdba1a5a561a879 ./Orussus_abietinus/trackList.json +35f9a1a800f0572ec5ce46fc6b12790b ./Osmia_lignaria/trackList.json +f81b350db3ea1a82a6d1253d7a0db8fb ./Pachypsylla_venusta/trackList.json +7c458ee03cbe372d5bd8ece05e65fefa ./Parasteatoda_tepidariorum/trackList.json +f4bb8abebb9f78d70bee481d19eb0d8d ./Photinus_pyralis/trackList.json +e71a903e88a05f21faccc3b02f7f67a3 ./Rhagoletis_zephyria/trackList.json +01f29c90f3798a7ceda00cfd97fabeae ./Rhipicephalus_microplus/trackList.json +a85c77319c20539a8a4dd52c9c1e2fcb ./Rhyzopertha_dominica/trackList.json +d674c41dcb573ad01801f1e486ba423c ./Saccharomyceseubayanus/trackList.json +83b29e7dd751971c1f1b824e262b3952 ./Tigriopus_californicus/trackList.json +bcf2ba9ed203eae9c0195c0695b0bee6 ./Tribolium_castaneum/trackList.json +6348ef622fab9ebe74cae8dac5cdbe07 ./Trichogramma_pretiosum/trackList.json +d695fd7a00f16e59ada39da2bc5b5a7c ./Varroa_destructor/trackList.json +98e6622539f46fa2c1770d329cace3d7 ./Varroa_jacobsoni/trackList.json diff --git a/organisms/stage/make_dir_and_cp_files.sh b/organisms/stage/make_dir_and_cp_files.sh new file mode 100644 index 0000000..6c851ef --- /dev/null +++ b/organisms/stage/make_dir_and_cp_files.sh @@ -0,0 +1,128 @@ +mkdir 10_-_Onthophagus_taurus_training; cd 10_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 11_-_Onthophagus_taurus_training; cd 11_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 12_-_Onthophagus_taurus_training; cd 12_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 13_-_Onthophagus_taurus_training; cd 13_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 14_-_Onthophagus_taurus_training; cd 14_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 15_-_Onthophagus_taurus_training; cd 15_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 16_-_Onthophagus_taurus_training; cd 16_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 17_-_Onthophagus_taurus_training; cd 17_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 18_-_Onthophagus_taurus_training; cd 18_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 19_-_Onthophagus_taurus_training; cd 19_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 1_-_Onthophagus_taurus_training; cd 1_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 20_-_Onthophagus_taurus_training; cd 20_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 21_-_Onthophagus_taurus_training; cd 21_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 22_-_Onthophagus_taurus_training; cd 22_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 23_-_Onthophagus_taurus_training; cd 23_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 24_-_Onthophagus_taurus_training; cd 24_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 25_-_Onthophagus_taurus_training; cd 25_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 26_-_Onthophagus_taurus_training; cd 26_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 27_-_Onthophagus_taurus_training; cd 27_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 28_-_Onthophagus_taurus_training; cd 28_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 29_-_Onthophagus_taurus_training; cd 29_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 2_-_Onthophagus_taurus_training; cd 2_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 30_-_Onthophagus_taurus_training; cd 30_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 31_-_Onthophagus_taurus_training; cd 31_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 32_-_Onthophagus_taurus_training; cd 32_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 33_-_Onthophagus_taurus_training; cd 33_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 34_-_Onthophagus_taurus_training; cd 34_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 35_-_Onthophagus_taurus_training; cd 35_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 36_-_Onthophagus_taurus_training; cd 36_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 37_-_Onthophagus_taurus_training; cd 37_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 38_-_Onthophagus_taurus_training; cd 38_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 39_-_Onthophagus_taurus_training; cd 39_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 3_-_Onthophagus_taurus_training; cd 3_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 40_-_Onthophagus_taurus_training; cd 40_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 4_-_Onthophagus_taurus_training; cd 4_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 5_-_Onthophagus_taurus_training; cd 5_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 6_-_Onthophagus_taurus_training; cd 6_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 7_-_Onthophagus_taurus_training; cd 7_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 8_-_Onthophagus_taurus_training; cd 8_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 9_-_Onthophagus_taurus_training; cd 9_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir Aethina_tumida; cd Aethina_tumida; cp /app/data/other_species/aettum/jbrowse/data/trackList.json .; cd .. +mkdir Agrilus_planipennis; cd Agrilus_planipennis; cp /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/trackList.json .; cd .. +mkdir Amyelois_transitella; cd Amyelois_transitella; cp /app/data/other_species/amytra/jbrowse/data/trackList.json .; cd .. +mkdir Anoplophora_glabripennis; cd Anoplophora_glabripennis; cp /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Apis_mellifera; cd Apis_mellifera; cp /app/data/other_species/apimel/Amel_4.5/jbrowse/data//trackList.json .; cd .. +mkdir Athalia_rosae; cd Athalia_rosae; cp /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Bactrocera_cucurbitae; cd Bactrocera_cucurbitae; cp /app/data/other_species/baccuc/jbrowse/data/trackList.json .; cd .. +mkdir Bactrocera_dorsalis; cd Bactrocera_dorsalis; cp /app/data/other_species/bacdor/jbrowse/data/trackList.json .; cd .. +mkdir Bactrocera_oleae; cd Bactrocera_oleae; cp /app/data/other_species/bacole/jbrowse/data/trackList.json .; cd .. +mkdir Bemisia_tabaci; cd Bemisia_tabaci; cp /app/data/other_species/bemtab/jbrowse/data/trackList.json .; cd .. +mkdir Blattella_germanica; cd Blattella_germanica; cp /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Bombus_impatiens; cd Bombus_impatiens; cp /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data/trackList.json .; cd .. +mkdir Bombus_terrestris; cd Bombus_terrestris; cp /app/data/other_species/bomter/Bter_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Bradysia_coprophila; cd Bradysia_coprophila; cp /app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data/trackList.json .; cd .. +mkdir Catajapyx_aquilonaris; cd Catajapyx_aquilonaris; cp /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/trackList.json .; cd .. +mkdir Centruroides_sculpturatus; cd Centruroides_sculpturatus; cp /app/data/BCM_i5k_pilot/censcu/jbrowse/data/trackList.json .; cd .. +mkdir Cephus_cinctus; cd Cephus_cinctus; cp /app/data/other_species/cepcin/Ccin1/jbrowse/data//trackList.json .; cd .. +mkdir Ceratitis_capitata; cd Ceratitis_capitata; cp /app/data/BCM_i5k_pilot/cercap/jbrowse/data/trackList.json .; cd .. +mkdir Chelonus_insularis; cd Chelonus_insularis; cp /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/trackList.json .; cd .. +mkdir Cimex_lectularius; cd Cimex_lectularius; cp /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Clitarchus_hookeri; cd Clitarchus_hookeri; cp /app/data/other_species/clihoo/jbrowse/data/trackList.json .; cd .. +mkdir Contarinia_nasturtii; cd Contarinia_nasturtii; cp /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/trackList.json .; cd .. +mkdir Copidosoma_floridanum; cd Copidosoma_floridanum; cp /app/data/BCM_i5k_pilot/copflo/jbrowse/data/trackList.json .; cd .. +mkdir Diabrotica_virgifera_training; cd Diabrotica_virgifera_training; cp /app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data/trackList.json .; cd .. +mkdir Diachasma_alloeum; cd Diachasma_alloeum; cp /app/data/other_species/diaall/Dall2.0/jbrowse/data/trackList.json .; cd .. +mkdir Diaphorina_citri; cd Diaphorina_citri; cp /app/data/other_species/diacit/jbrowse/data/trackList.json .; cd .. +mkdir Diaphorina_citri_legacy; cd Diaphorina_citri_legacy; cp /app/data/other_species/diacit_legacy/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_biarmipes; cd Drosophila_biarmipes; cp /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_bipectinata; cd Drosophila_bipectinata; cp /app/data/modencode/drobip/Dbip_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_elegans; cd Drosophila_elegans; cp /app/data/modencode/droele/Dele_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_eugracilis; cd Drosophila_eugracilis; cp /app/data/modencode/droeug/Deug_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_ficusphila; cd Drosophila_ficusphila; cp /app/data/modencode/drofic/Dfic_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_kikkawai; cd Drosophila_kikkawai; cp /app/data/modencode/drokik/Dkik_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_rhopaloa; cd Drosophila_rhopaloa; cp /app/data/modencode/drorho/Drho_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_takahashii; cd Drosophila_takahashii; cp /app/data/modencode/drotak/Dtak_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Dufourea_novaeangliae; cd Dufourea_novaeangliae; cp /app/data/other_species/dufnov/jbrowse/data/trackList.json .; cd .. +mkdir Ephemera_danica; cd Ephemera_danica; cp /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data//trackList.json .; cd .. +mkdir Eufriesea_mexicana; cd Eufriesea_mexicana; cp /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/trackList.json .; cd .. +mkdir Euglossa_dilemma; cd Euglossa_dilemma; cp /app/data/other_species/eugdil/jbrowse/data/trackList.json .; cd .. +mkdir Eurytemora_affinis; cd Eurytemora_affinis; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. +mkdir Eurytemora_affinis_-_training; cd Eurytemora_affinis_-_training; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. +mkdir Fopius_arisanus; cd Fopius_arisanus; cp /app/data/other_species/fopari/jbrowse/data/trackList.json .; cd .. +mkdir Frankliniella_occidentalis; cd Frankliniella_occidentalis; cp /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/trackList.json .; cd .. +mkdir Galleria_mellonella; cd Galleria_mellonella; cp /app/data/other_species/galmel/ASM364042v2/jbrowse/data/trackList.json .; cd .. +mkdir Gerris_buenoi; cd Gerris_buenoi; cp /app/data/BCM_i5k_pilot/gerbue/jbrowse/data//trackList.json .; cd .. +mkdir Habropoda_laboriosa; cd Habropoda_laboriosa; cp /app/data/other_species/hablab/jbrowse/data/trackList.json .; cd .. +mkdir Halyomorpha_halys; cd Halyomorpha_halys; cp /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/trackList.json .; cd .. +mkdir Heliothis_virescens; cd Heliothis_virescens; cp /app/data/other_species/helvir/jbrowse/data//trackList.json .; cd .. +mkdir Holacanthella_duospinosa; cd Holacanthella_duospinosa; cp /app/data/other_species/holduo/ASM273828v1/jbrowse/data/trackList.json .; cd .. +mkdir Homalodisca_vitripennis; cd Homalodisca_vitripennis; cp /app/data/BCM_i5k_pilot/homvit/jbrowse/data/trackList.json .; cd .. +mkdir Hyalella_azteca; cd Hyalella_azteca; cp /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/trackList.json .; cd .. +mkdir Laodelphax_striatellus; cd Laodelphax_striatellus; cp /app/data/other_species/laostr/ASM333518v2/jbrowse/data/trackList.json .; cd .. +mkdir Lasioglossum_albipes; cd Lasioglossum_albipes; cp /app/data/other_species/lasalb/jbrowse/data/trackList.json .; cd .. +mkdir Latrodectus_hesperus; cd Latrodectus_hesperus; cp /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/trackList.json .; cd .. +mkdir Leptinotarsa_decemlineata; cd Leptinotarsa_decemlineata; cp /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Leptinotarsa_decemlineata_training; cd Leptinotarsa_decemlineata_training; cp /app/data/BCM_i5k_pilot/lepdec/jbrowse/data/trackList.json .; cd .. +mkdir Limnephilus_lunatus; cd Limnephilus_lunatus; cp /app/data/BCM_i5k_pilot/limlun/jbrowse/data/trackList.json .; cd .. +mkdir Locusta_migratoria; cd Locusta_migratoria; cp /app/data/other_species/locmig/jbrowse/data//trackList.json .; cd .. +mkdir Loxosceles_reclusa; cd Loxosceles_reclusa; cp /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data/trackList.json .; cd .. +mkdir Mamestra_configurata; cd Mamestra_configurata; cp /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/trackList.json .; cd .. +mkdir Manduca_sexta; cd Manduca_sexta; cp /app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data/trackList.json .; cd .. +mkdir Mayetiola_destructor; cd Mayetiola_destructor; cp /app/data/other_species/maydes/jbrowse/data/trackList.json .; cd .. +mkdir Medauroidea_extradentata; cd Medauroidea_extradentata; cp /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/trackList.json .; cd .. +mkdir Megachile_rotundata; cd Megachile_rotundata; cp /app/data/other_species/megrot/jbrowse/data/trackList.json .; cd .. +mkdir Melipona_quadrifasciata; cd Melipona_quadrifasciata; cp /app/data/other_species/melqua/jbrowse/data/trackList.json .; cd .. +mkdir Microplitis_demolitor; cd Microplitis_demolitor; cp /app/data/other_species/micdem/jbrowse/data/trackList.json .; cd .. +mkdir Neodiprion_lecontei; cd Neodiprion_lecontei; cp /app/data/other_species/neolec/Nlec1.1/jbrowse/data/trackList.json .; cd .. +mkdir Neodiprion_lecontei_training; cd Neodiprion_lecontei_training; cp /app/data/other_species/neolec/jbrowse/data/trackList.json .; cd .. +mkdir Nicrophorus_vespilloides; cd Nicrophorus_vespilloides; cp /app/data/other_species/nicves/jbrowse/data/trackList.json .; cd .. +mkdir Nylanderia_fulva; cd Nylanderia_fulva; cp /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Odontomachus_brunneus; cd Odontomachus_brunneus; cp /app/data/other_species/odobru/Obru_v1/jbrowse/data/trackList.json .; cd .. +mkdir Oncopeltus_fasciatus; cd Oncopeltus_fasciatus; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. +mkdir Oncopeltus_fasciatus_training; cd Oncopeltus_fasciatus_training; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. +mkdir Onthophagus_taurus; cd Onthophagus_taurus; cp /app/data/BCM_i5k_pilot/onttau/jbrowse/data/trackList.json .; cd .. +mkdir Orussus_abietinus; cd Orussus_abietinus; cp /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Osmia_lignaria; cd Osmia_lignaria; cp /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Pachypsylla_venusta; cd Pachypsylla_venusta; cp /app/data/BCM_i5k_pilot/pacven/jbrowse/data/trackList.json .; cd .. +mkdir Parasteatoda_tepidariorum; cd Parasteatoda_tepidariorum; cp /app/data/BCM_i5k_pilot/partep/jbrowse/data/trackList.json .; cd .. +mkdir Photinus_pyralis; cd Photinus_pyralis; cp /app/data/other_species/phopyr/Ppyr1.3/jbrowse/data/trackList.json .; cd .. +mkdir Rhagoletis_zephyria; cd Rhagoletis_zephyria; cp /app/data/other_species/rhazep/jbrowse/data/trackList.json .; cd .. +mkdir Rhipicephalus_microplus; cd Rhipicephalus_microplus; cp /app/data/other_species/rhimic/jbrowse/data/trackList.json .; cd .. +mkdir Rhyzopertha_dominica; cd Rhyzopertha_dominica; cp /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/trackList.json .; cd .. +mkdir Saccharomyceseubayanus; cd Saccharomyceseubayanus; cp /app/data/other_species/saceub/SEUB3.0/jbrowse/data/trackList.json .; cd .. +mkdir Tigriopus_californicus; cd Tigriopus_californicus; cp /app/data/other_species/tigcal/jbrowse/data/trackList.json .; cd .. +mkdir Tribolium_castaneum; cd Tribolium_castaneum; cp /app/data/other_species/tricas/jbrowse/data/trackList.json .; cd .. +mkdir Trichogramma_pretiosum; cd Trichogramma_pretiosum; cp /app/data/BCM_i5k_pilot/tripre/jbrowse/data/trackList.json .; cd .. +mkdir Varroa_destructor; cd Varroa_destructor; cp /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/trackList.json .; cd .. +mkdir Varroa_jacobsoni; cd Varroa_jacobsoni; cp /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/trackList.json .; cd .. diff --git a/organisms/stage/make_dir_script.pl b/organisms/stage/make_dir_script.pl new file mode 100644 index 0000000..5b2aa5f --- /dev/null +++ b/organisms/stage/make_dir_script.pl @@ -0,0 +1,9 @@ +#!/usr/bin/perl -w + +use strict; + +while (<>){ + $_ =~ m/(\S*)\|(\S*)/; + print "mkdir $1; cd $1; cp $2/trackList.json .; cd .. \n"; +} + diff --git a/organisms/stage/organism_list.txt2 b/organisms/stage/organism_list.txt2 new file mode 100644 index 0000000..54691ba --- /dev/null +++ b/organisms/stage/organism_list.txt2 @@ -0,0 +1,128 @@ +10_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +11_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +12_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +13_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +14_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +15_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +16_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +17_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +18_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +19_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +1_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +20_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +21_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +22_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +23_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +24_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +25_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +26_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +27_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +28_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +29_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +2_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +30_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +31_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +32_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +33_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +34_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +35_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +36_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +37_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +38_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +39_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +3_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +40_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +4_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +5_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +6_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +7_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +8_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +9_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +Aethina_tumida|/app/data/other_species/aettum/jbrowse/data +Agrilus_planipennis|/app/data/BCM_i5k_pilot/agrpla/jbrowse/data +Amyelois_transitella|/app/data/other_species/amytra/jbrowse/data +Anoplophora_glabripennis|/app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data +Apis_mellifera|/app/data/other_species/apimel/Amel_4.5/jbrowse/data/ +Athalia_rosae|/app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data +Bactrocera_cucurbitae|/app/data/other_species/baccuc/jbrowse/data +Bactrocera_dorsalis|/app/data/other_species/bacdor/jbrowse/data +Bactrocera_oleae|/app/data/other_species/bacole/jbrowse/data +Bemisia_tabaci|/app/data/other_species/bemtab/jbrowse/data +Blattella_germanica|/app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data +Bombus_impatiens|/app/data/other_species/bomimp/BIMP_2.1/jbrowse/data +Bombus_terrestris|/app/data/other_species/bomter/Bter_1.0/jbrowse/data +Bradysia_coprophila|/app/data/other_species/bracop/BU_Bcop_v1/jbrowse/data +Catajapyx_aquilonaris|/app/data/BCM_i5k_pilot/cataqu/jbrowse/data +Centruroides_sculpturatus|/app/data/BCM_i5k_pilot/censcu/jbrowse/data +Cephus_cinctus|/app/data/other_species/cepcin/Ccin1/jbrowse/data/ +Ceratitis_capitata|/app/data/BCM_i5k_pilot/cercap/jbrowse/data +Chelonus_insularis|/app/data/other_species/cheins/ASM1335770v1/jbrowse/data +Cimex_lectularius|/app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data +Clitarchus_hookeri|/app/data/other_species/clihoo/jbrowse/data +Contarinia_nasturtii|/app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data +Copidosoma_floridanum|/app/data/BCM_i5k_pilot/copflo/jbrowse/data +Diabrotica_virgifera_training|/app/data/other_species/diavir/Dvir_v2.0_RefSeq/jbrowse/data +Diachasma_alloeum|/app/data/other_species/diaall/Dall2.0/jbrowse/data +Diaphorina_citri|/app/data/other_species/diacit/jbrowse/data +Diaphorina_citri_legacy|/app/data/other_species/diacit_legacy/jbrowse/data +Drosophila_biarmipes|/app/data/modencode/drobia/Dbia_2.0/jbrowse/data +Drosophila_bipectinata|/app/data/modencode/drobip/Dbip_2.0/jbrowse/data +Drosophila_elegans|/app/data/modencode/droele/Dele_2.0/jbrowse/data +Drosophila_eugracilis|/app/data/modencode/droeug/Deug_2.0/jbrowse/data +Drosophila_ficusphila|/app/data/modencode/drofic/Dfic_2.0/jbrowse/data +Drosophila_kikkawai|/app/data/modencode/drokik/Dkik_2.0/jbrowse/data +Drosophila_rhopaloa|/app/data/modencode/drorho/Drho_2.0/jbrowse/data +Drosophila_takahashii|/app/data/modencode/drotak/Dtak_2.0/jbrowse/data +Dufourea_novaeangliae|/app/data/other_species/dufnov/jbrowse/data +Ephemera_danica|/app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ +Eufriesea_mexicana|/app/data/other_species/eufmex/ASM148370v1/jbrowse/data +Euglossa_dilemma|/app/data/other_species/eugdil/jbrowse/data +Eurytemora_affinis|/app/data/BCM_i5k_pilot/euraff/jbrowse/data +Eurytemora_affinis_-_training|/app/data/BCM_i5k_pilot/euraff/jbrowse/data +Fopius_arisanus|/app/data/other_species/fopari/jbrowse/data +Frankliniella_occidentalis|/app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data +Galleria_mellonella|/app/data/other_species/galmel/ASM364042v2/jbrowse/data +Gerris_buenoi|/app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ +Habropoda_laboriosa|/app/data/other_species/hablab/jbrowse/data +Halyomorpha_halys|/app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data +Heliothis_virescens|/app/data/other_species/helvir/jbrowse/data/ +Holacanthella_duospinosa|/app/data/other_species/holduo/ASM273828v1/jbrowse/data +Homalodisca_vitripennis|/app/data/BCM_i5k_pilot/homvit/jbrowse/data +Hyalella_azteca|/app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data +Laodelphax_striatellus|/app/data/other_species/laostr/ASM333518v2/jbrowse/data +Lasioglossum_albipes|/app/data/other_species/lasalb/jbrowse/data +Latrodectus_hesperus|/app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data +Leptinotarsa_decemlineata|/app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data +Leptinotarsa_decemlineata_training|/app/data/BCM_i5k_pilot/lepdec/jbrowse/data +Limnephilus_lunatus|/app/data/BCM_i5k_pilot/limlun/jbrowse/data +Locusta_migratoria|/app/data/other_species/locmig/jbrowse/data/ +Loxosceles_reclusa|/app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data +Mamestra_configurata|/app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data +Manduca_sexta|/app/data/other_species/mansex/JHU_Msex_v1.0/jbrowse/data +Mayetiola_destructor|/app/data/other_species/maydes/jbrowse/data +Medauroidea_extradentata|/app/data/other_species/medext/GCA_003012365.1/jbrowse/data +Megachile_rotundata|/app/data/other_species/megrot/jbrowse/data +Melipona_quadrifasciata|/app/data/other_species/melqua/jbrowse/data +Microplitis_demolitor|/app/data/other_species/micdem/jbrowse/data +Neodiprion_lecontei|/app/data/other_species/neolec/Nlec1.1/jbrowse/data +Neodiprion_lecontei_training|/app/data/other_species/neolec/jbrowse/data +Nicrophorus_vespilloides|/app/data/other_species/nicves/jbrowse/data +Nylanderia_fulva|/app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data +Odontomachus_brunneus|/app/data/other_species/odobru/Obru_v1/jbrowse/data +Oncopeltus_fasciatus|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data +Oncopeltus_fasciatus_training|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data +Onthophagus_taurus|/app/data/BCM_i5k_pilot/onttau/jbrowse/data +Orussus_abietinus|/app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data +Osmia_lignaria|/app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data +Pachypsylla_venusta|/app/data/BCM_i5k_pilot/pacven/jbrowse/data +Parasteatoda_tepidariorum|/app/data/BCM_i5k_pilot/partep/jbrowse/data +Photinus_pyralis|/app/data/other_species/phopyr/Ppyr1.3/jbrowse/data +Rhagoletis_zephyria|/app/data/other_species/rhazep/jbrowse/data +Rhipicephalus_microplus|/app/data/other_species/rhimic/jbrowse/data +Rhyzopertha_dominica|/app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data +Saccharomyceseubayanus|/app/data/other_species/saceub/SEUB3.0/jbrowse/data +Tigriopus_californicus|/app/data/other_species/tigcal/jbrowse/data 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Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "File note" : "This track replaces the previous track, 'Aros_ID06'.", + "Alignment method" : "TopHat 2.0, default parameters", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Data Provider" : "Baylor College of Medicine" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "Aros_ID06", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae female-2 raw reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/Aros_ID07.bam", + "metadata" : { + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/DFED2491-A36F-41E0-BE8B-DDEDAE6050FD/align_summary.txt", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "File note" : "This track replaces the previous track, 'Aros_ID07'.", + "Alignment method" : "TopHat 2.0, default parameters", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Data Provider" : "Baylor College of Medicine" + }, + "label" : "Aros_ID07", + "type" : "WebApollo/View/Track/DraggableAlignments", + "category" : "Transcriptome/Mapped Reads", + "key" : "A. rosae male-2 raw reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/Aros_ID08.bam", + "metadata" : { + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C72E8FAE-2A8F-48CC-8E81-E763757DC126/align_summary.txt", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "File note" : "This track replaces the previous track, 'Aros_ID08'.", + "Alignment method" : "TopHat 2.0, default parameters", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Data Provider" : "Baylor College of Medicine" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "Aros_ID08", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae male-1 raw reads" + }, + { + "style" : { + "neg_color" : "rgba(255,255,0,50)", + "pos_color" : "rgba(0,0,255,50)" + }, + "bicolor_pivot" : "0.5", + "key" : "GC Content", + "scoreType": "avgScore", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Aros01112013-genome_GC.bigwig", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track contact" : "The i5k workspace@NAL" + }, + "type" : "JBrowse/View/Track/Wiggle/Density", + "label" : "GC Content" + }, + { + "style" : { + "neg_color" : "white", + "pos_color" : "black" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "key" : "Gaps in assembly", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Aros01112013-GAPS.bigwig", + "label" : "Gaps in assembly", + "metadata" : { + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track contact" : "The i5k workspace@NAL" + }, + "category" : "Reference Assembly", + "type" : "JBrowse/View/Track/Wiggle/Density" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "A. rosae females-combined Trinity transcriptome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/atro-females-comb_est2genome/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads from two females were concatenated and then assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Assembly", + "label" : "atro-females-comb_est2genome", + "type" : "FeatureTrack" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "A. rosae male-1 Trinity transcriptome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/atro-male-1_est2genome/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Assembly", + "label" : "atro-male-1_est2genome", + "type" : "FeatureTrack" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "A. rosae male-2 Trinity transcriptome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/atro-male-2_est2genome/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Assembly", + "label" : "atro-male-2_est2genome", + "type" : "FeatureTrack" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_male-1_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae male-1 cleaned reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-2_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_male-2_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae male-2 cleaned reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_female-1_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae female-1 cleaned reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 " + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_female-2_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae female-2 cleaned reads" + }, + { + "style" : { + "clip_marker_color" : "red", + "pos_color" : "#FFA600", + "neg_color" : "#005EFF", + "height" : 50 + }, + "bicolor_pivot" : "zero", + "key" : " A. rosae female-1 cleaned reads, XY-plots", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bigwig", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Coverage plots (BigWig)", + "label" : "aros_female-1_tophat-accepted_hits_bigwig" + }, + { + "style" : { + "clip_marker_color" : "red", + "pos_color" : "#FFA600", + "neg_color" : "#005EFF", + "height" : 50 + }, + "bicolor_pivot" : "zero", + "key" : " A. rosae female-2 cleaned reads, XY-plots", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bigwig", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 " + }, + "category" : "Transcriptome/Coverage plots (BigWig)", + "label" : "aros_female-2_tophat-accepted_hits_bigwig" + }, + { + "style" : { + "clip_marker_color" : "red", + "pos_color" : "#FFA600", + "neg_color" : "#005EFF", + "height" : 50 + }, + "bicolor_pivot" : "zero", + "key" : " A. rosae male-1 cleaned reads, XY-plots", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bigwig", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine" + } + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "protein2genome_Tardigrada", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "label" : "protein2genome_Tardigrada", + "type" : "FeatureTrack", + "category" : "BCM_v0.5.3/3. 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At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track contact" : "The i5k workspace@NAL" + } + }, + { + "style" : { + "pos_color" : "#00BFFF", + "neg_color" : "BG_RNAseq_heads_NCSU" + }, + "bicolor_pivot" : "zero", + "key" : "BG_RNAseq_heads_NCSU", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/TopHat2-SE_Lane1_2_Sample3_4_merged-2015-09-01-21-37-00.7/TopHat2-SE_Lane1_2_Sample3_4_merged.bam", + "metadata" : { + "RNA dataset name" : "BG_RNAseq_heads_NCSU", + "Species name" : "Blattella germanica", + "Data Source 3 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/BF73CC50-6318-4461-B672-6C83180CEA43/align_summary.txt", + "Note" : "This is merged dataset from four separate sources", + "Data Source 2 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/C417CB73-E609-49FB-89CC-EEA20455B734/align_summary.txt", + "Data Source 4 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/DAA3D4D7-4D22-451D-9914-EAD37D2E0A5B/align_summary.txt", + "Data Source 1 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/040B27B4-069D-4B29-9F17-851270ED0534/align_summary.txt", + "Data Provider" : "Coby Schal, NCSU" + }, + "type" : "WebApollo/View/Track/DraggableAlignments", + "category" : "Transcriptome/Mapped Reads", + "label" : "BG_RNAseq_heads_NCSU" + }, + { + "style" : { + "neg_color" : "BG_RNAseq_heads_NCSU", + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "key" : "BG_RNAseq_heads_NCSU (Coverage Plot)", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/TopHat2-SE_Lane1_2_Sample3_4_merged-2015-09-01-21-37-00.7/TopHat2-SE_Lane1_2_Sample3_4_merged.bigwig", + "metadata" : { + "RNA dataset name" : "BG_RNAseq_heads_NCSU", + "Species name" : "Blattella germanica", + "Data Source 3 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/BF73CC50-6318-4461-B672-6C83180CEA43/align_summary.txt", + "Note" : "This is merged dataset from four separate sources", + "Data Source 2 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/C417CB73-E609-49FB-89CC-EEA20455B734/align_summary.txt", + "Data Source 4 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/DAA3D4D7-4D22-451D-9914-EAD37D2E0A5B/align_summary.txt", + "Data Source 1 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/040B27B4-069D-4B29-9F17-851270ED0534/align_summary.txt", + "Data Provider" : "Coby Schal, NCSU" + }, + "label" : "BG_RNAseq_heads_NCSU (Coverage Plot)", + "category" : "Transcriptome/Coverage Plots (BigWig)", + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/SRR1552487_SRR1552488_merged-2015-09-01-18-15-30.1/SRR1552487_SRR1552488_merged.bam", + "label" : "BG_RNAseq_heads_UW", + "type" : "WebApollo/View/Track/DraggableAlignments", + "category" : "Transcriptome/Mapped Reads", + "metadata" : { + "Data URL" : "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488", + "Alignment summary" : "PE_SRR1552487: http://de.iplantcollaborative.org/dl/d/C663364F-AAA3-427F-8DFD-27772ED2BDCB/align_summary.txt; PE_SRR1552488: http://de.iplantcollaborative.org/dl/d/908426A6-7915-4CB4-9EA7-ABDA19590C4F/align_summary.txt", + "Other notes" : "tophat parameters: PE_SRR1552487: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552487_read1.fastq' --file_query2 'SRR1552487_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'; PE_SRR1552488: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552488_read1.fastq' --file_query2 'SRR1552488_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'", + "Citation" : "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700", + "File provider" : "Kim Walden, UIUC", + "Data provider" : "Inez Anna Drinnenberg", + "Track legend" : "Reads from SRR1552487 and SRR1552488 were aligned to the B. germanica assembly in TopHat, and the resulting alignment files were merged. Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "key" : "BG_RNAseq_heads_UW" + }, + { + "style" : { + "pos_color" : "#00BFFF", + "neg_color" : "BG_RNAseq_heads_UW" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "key" : "BG_RNAseq_heads_UW (Coverage Plot)", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/SRR1552487_SRR1552488_merged-2015-09-01-18-15-30.1/SRR1552487_SRR1552488_merged-nosecondary.bigwig", + "metadata" : { + "Data URL" : "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488", + "Other notes" : "tophat parameters: PE_SRR1552487: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552487_read1.fastq' --file_query2 'SRR1552487_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'; PE_SRR1552488: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552488_read1.fastq' --file_query2 'SRR1552488_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'", + "Alignment summary" : "PE_SRR1552487: http://de.iplantcollaborative.org/dl/d/C663364F-AAA3-427F-8DFD-27772ED2BDCB/align_summary.txt; PE_SRR1552488: http://de.iplantcollaborative.org/dl/d/908426A6-7915-4CB4-9EA7-ABDA19590C4F/align_summary.txt", + "File provider" : "Kim Walden, UIUC", + "Citation" : "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700", + "Data provider" : "Inez Anna Drinnenberg", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "blastx_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. 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Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "repeatmasker", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatmasker" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "repeatrunner", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatrunner" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "snap" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions", + "metadata" : { + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "snap_masked", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "snap_masked" + }, + { + "style" : { + "pos_color" : "black", + "neg_color" : "white" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank", + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", +}, + "key" : "Gaps in assembly", + + + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Gbue.scaffolds.50.fa.gaps.bigwig", + "label" : "Gaps in assembly", + "type" : "JBrowse/View/Track/Wiggle/Density" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/darmisen/Gbue_ICD_GBi5AK.bam", + "metadata" : { + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
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Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "est2genome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "category" : "BCM_v0.5.3/3. Mapped DNA/Other", + "urlTemplate" : "tracks/est2genome/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est2genome" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use.", + "Source data" : "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP028/SRP028964/SRR955076/SRR955076.sra", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "alignment summary" : "http://de.iplantcollaborative.org/dl/d/0AD340BA-F2AC-4E60-BCD3-7082201ED087/align_summary.txt" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/Microplitis_demolitor/Microplitis_demolitor_teratocytes_accepted_hits_refSeq_IDs.bigwig" + }, + { + "category" : "Mapped DNA/Microplitis demolitor ovary DNA", + "key" : "Microplitis demolitor ovary DNA, mapped reads", + "label" : "Microplitis demolitor ovary DNA, mapped reads", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739298/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420507", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1128/JVI.01388-15", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/3t4wo_sort.bam" + }, + { + "category" : "Mapped DNA/Microplitis demolitor bracovirus DNA", + "key" : "Microplitis demolitor bracovirus DNA, mapped reads", + "label" : "Microplitis demolitor bracovirus DNA, mapped reads", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739297/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420508", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/mdbv_all_sort.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Microplitis demolitor ovary DNA", + "key" : "Microplitis demolitor ovary DNA (Coverage Plot)", + "label" : "Microplitis demolitor ovary DNA (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739298/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420507", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1128/JVI.01388-15", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/3t4wo_sort.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Microplitis demolitor bracovirus DNA", + "key" : "Microplitis demolitor bracovirus DNA (Coverage Plot)", + "label" : "Microplitis demolitor bracovirus DNA (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739297/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420508", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/mdbv_all_sort.bigwig" + }, + { + "category" : "Mapped DNA/Mapped Reads", + "key" : "Infected Chrysodeixis includens hemocytes", + "label" : "Infected Chrysodeixis includens hemocytes", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739316/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRX1047183/", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_hemo_sort_mdbv.bam" + }, + { + "category" : "Mapped DNA/Mapped Reads", + "key" : "Infected Chrysodeixis includens", + "label" : "Infected Chrysodeixis includens", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739318", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766325,SRX3766326,SRX3766328,SRX3766330,SRX3766333,SRX3766334", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_sort_mdbv.bam" + }, + { + "category" : "Mapped DNA/Mapped Reads", + "key" : "Infected Trichoplusia ni", + "label" : "Infected Trichoplusia ni", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739317/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766323,SRX3766324,SRX3766327,SRX3766329,SRX3766331,SRX3766332", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/t_sort_mdbv.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Coverage Plots (BigWig)", + "key" : "Infected Chrysodeixis includens hemocytes (Coverage Plot)", + "label" : "Infected Chrysodeixis includens hemocytes (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739316/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRX1047183/", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_hemo_sort_mdbv.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Coverage Plots (BigWig)", + "key" : "Infected Chrysodeixis includens (Coverage Plot)", + "label" : "Infected Chrysodeixis includens (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739318", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766325,SRX3766326,SRX3766328,SRX3766330,SRX3766333,SRX3766334", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_sort_mdbv.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Coverage Plots (BigWig)", + "key" : "Infected Trichoplusia ni (Coverage Plot)", + "label" : "Infected Trichoplusia ni (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739317", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766323,SRX3766324,SRX3766327,SRX3766329,SRX3766331,SRX3766332", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/t_sort_mdbv.bigwig" + }, + { + "category" : "Mapped DNA/Microplitis demolitor ovary DNA", + "key" : "Microplitis demolitor ovary DNA, mapped reads (1% coverage)", + "label" : "Microplitis demolitor ovary DNA, mapped reads (1% coverage)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739298/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420507", + "Method" : "bwa 0.7.15; Coverage reduced to 1% with GATK", + "Publication status" : "Published - please cite 10.1128/JVI.01388-15", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/3t4wo_sort.RG.Reordered.RCfrac.bam" + }, + { + "category" : "Mapped DNA/Microplitis demolitor bracovirus DNA", + "key" : "Microplitis demolitor bracovirus DNA, mapped reads (0.1% coverage)", + "label" : "Microplitis demolitor bracovirus DNA, mapped reads (0.1% coverage)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739297/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420508", + "Method" : "bwa 0.7.15; Coverage reduced to 0.1% with GATK", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Lauderdale conditions of data re-use.", + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "snap" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "pooled RNA-seq - cleaned reads", + "label" : "pooled_RNA-seq_cleaned_reads", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. 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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Nematomorpha", + "label" : "protein2genome_Nematomorpha", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Onychophora", + "label" : "protein2genome_Onychophora", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Parazoa", + "label" : "protein2genome_Parazoa", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Placozoa", + "label" : "protein2genome_Placozoa", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Platyhelminthes", + "label" : "protein2genome_Platyhelminthes", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Priapulida", + "label" : "protein2genome_Priapulida", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Tardigrada", + "label" : "protein2genome_Tardigrada", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Tunicata", + "label" : "protein2genome_Tunicata", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_UNCATEGORISED", + "label" : "protein2genome_UNCATEGORISED", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/2. 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Evidence/Repeats", + "compress" : 0, + "key" : "repeatrunner", + "label" : "repeatrunner", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "repeat" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/1. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "snap" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "pooled RNA-seq - cleaned reads", + "label" : "pooled_RNA-seq_cleaned_reads", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "bam/ivargas/cleaned_reads/accepted_hits.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "RNA-Seq/Coverage Plots", + "key" : "pooled RNA-seq - cleaned reads, XY-plot", + "label" : "pooled RNA-seq - cleaned reads, XY-plot", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "clip_marker_color" : "red", + "height" : 50, + "neg_color" : "#005EFF", + "pos_color" : "#FFA600" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "bam/ivargas/cleaned_reads/accepted_hits.bigwig" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "pooled RNA-seq - raw reads", + "label" : "pooled_RNA-seq_raw_reads", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/653A7172-438A-4688-811C-FA92A8FD22E6/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "bam/ivargas/raw_reads/accepted_hits.bam" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "RNA-seq raw PE reads Andolfatto et al.", + "label" : "RNA-seq_Andolfatto_raw_PE_reads", + "metadata" : { + "Alignment method" : "--align_reads together --mate-inner-dist 50 --file_query Oncopeltus_fasciatus_PE_1.fq.gz --file_query2 Oncopeltus_fasciatus_PE_2.fq.gz --library-type fr-unstranded --min-anchor-length 8 --splice-mismatches 0 --min-intron-length 70 --max-intron-length 50000 --min-isoform-fraction 0.15 --max-multihits 20 --min-segment-intron 50 --max-segment-intron 500000 --segment-mismatches 2 --segment-length 20 --num-threads 6 --user_database Ofas.scaffolds.fa --b2-sensitive --tophat_version 2.0.9 --bowtie_version 2.1.0", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/5671A470-68E8-4FF2-AA8F-B55A8CC74AFF/align_summary.txt", + "Data Source" : "http://genomics-pubs.princeton.edu/insect_genomics/data/Oncopeltus_fasciatus.tar", + "Read cleaning method" : "None", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Green - insertion in the read relative to the reference
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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est-gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "repeatmasker", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatmasker" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "repeatrunner", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatrunner" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "snap" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions", + "metadata" : { + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "snap_masked", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "snap_masked" + }, + { + "style" : { + "className" : "container-16px", + "subfeatureClasses" : { + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "transcriptome-cds", + "UTR" : "transcriptome-utr" + }, + "arrowheadClass" : "trellis-arrowhead" + }, + "key" : "Jpn_Pt_gene.model_oda", + "category" : "Transcriptome/Assembly", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/Jpn_Pt_gene.model_oda/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Analysis method" : "Mapped the RNA-seq reads to Baylor's Pt-genome (Ptep01282013genome) with BLAT, and predicted genes and transcripts with cufflinks and cuffmerge using the RNA-seq mapping data together with EST and cDNA mapping data. We removed multiple-hit (>= 3) reads and one (scaffold with larger number) of two loci of two-hit reads", + "Data provider" : "Yasuko Akiyama-Oda and Hiroki Oda, JT Biohistory Research Hall", + "Source of materials" : "RNA-seq of embryonic libraries (stages 3, 5, 7, and 10)", + "Track information" : "Gene models predicted by Cufflinks/Cuffmerge based on mapping of RNA-seq reads" + }, + "type" : "FeatureTrack", + "label" : "Jpn_Pt_gene.model_oda" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "user_contributed_files/yaoda/EST_cDNA_Oda.bam", + "label" : "EST_oda", + "category" : "Transcriptome/Mapped ESTs", + "type" : "WebApollo/View/Track/DraggableAlignments", + "metadata" : { + "Accession number" : "The EST data are deposited in the DNA Data Bank of Japan under accession numbers FY216297–FY225483 and FY368221–FY381845.", + "Data provider" : "Yasuko Akiyama-Oda and Hiroki Oda, JT Biohistory Research Hall", + "Source of materials" : "The EST data are derived from the 5′ end of five P. tepidariorum embryo cDNA libraries at different stages: At_eW: mixed segmentation stages; eS6: early stage 6; eS7: early stage 7; S7: stage 7. The cDNA data are mostly from cDNAs cloned and sequenced in our laboratory but include several cDNAs retrieved from NCBI.", + "Track legend" : "This track is displayed so that aligned exons are colored in dark blue while the introns spanning the predicted splicing sites are light blue.", + "Track information" : "cDNA and EST data mapped with BLAT" + }, + "key" : "EST_oda" + }, + { + "style" : { + "pos_color" : "black", + "neg_color" : "white" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank", + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", +}, + "key" : "Gaps in assembly", + + + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Ptep01282013.GAPS.bigwig", + "label" : "Gaps in assembly", + "type" : "JBrowse/View/Track/Wiggle/Density" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Ptep01282013.genome_GC.bigwig", + "style" : { + "neg_color" : "rgba(255,255,0,50)", + "pos_color" : "rgba(0,0,255,50)" + }, + "label" : "GC Content", + "type" : "JBrowse/View/Track/Wiggle/Density", + "bicolor_pivot" : "0.5", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", +}, + "key" : "GC Content", + "scoreType": "avgScore", + + + "autoscale" : "local" + } + ], + "plugins" : [ + { + "location" : "./plugins/WebApollo", + "name" : "WebApollo" + } + ], + "names" : { + "url" : "names/", + "type" : "Hash" + }, + "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico", + "formatVersion" : 1, + "alwaysOnTracks" : "DNA,Annotations" +} diff --git a/organisms_orig/README b/organisms_orig/README new file mode 100644 index 0000000..90412f0 --- /dev/null +++ b/organisms_orig/README @@ -0,0 +1,30 @@ +# added -----COMPLETE +# "scoreType" : "avgScore", to the onttau training instances + +# perl -pi -e "s/ \"storeClass\" \: \"JBrowse\/Store\/SeqFeature\/BigWig\"\,\n/ \"storeClass\" \: \"JBrowse\/Store\/SeqFeature\/BigWig\",\n \"scoreType\" : \"avgScore\",\n/g" 2*_-_Onthophagus_taurus_training/trackList.json less 20_-_Onthophagus_taurus_training/trackList.json + +# These are the files that need to have ColorByType tracks. These will need to be replaced with the new track type +# grep -c ColorByType ./*/*|grep -v ":0" +# ./Apis_mellifera/trackList.json:2 +# ./Bombus_impatiens/trackList.json:3 +# ./Bombus_terrestris/trackList.json:3 +# ./Cephus_cinctus/trackList.json:4 +# ./Chelonus_insularis/trackList.json:2 +# ./Contarinia_nasturtii/trackList.json:2 +# ./Diachasma_alloeum/trackList.json:2 +# ./Ephemera_danica/trackList.json:2 +# ./Eufriesea_mexicana/trackList.json:2 +# ./Frankliniella_occidentalis/trackList.json:2 +# ./Galleria_mellonella/trackList.json:2 +# ./Halyomorpha_halys/trackList.json:2 +# ./Hyalella_azteca/trackList.json:2 +# ./Laodelphax_striatellus/trackList.json:2 +# ./Manduca_sexta/trackList.json:2 +# ./Neodiprion_lecontei/trackList.json:4 +# ./Nylanderia_fulva/trackList.json:2 +# ./Odontomachus_brunneus/trackList.json:2 +# ./Osmia_lignaria/trackList.json:2 +# ./Varroa_destructor/trackList.json:2 +# ./Varroa_jacobsoni/trackList.json:2 + +# Also need to make sure the css has been update=d diff --git a/organisms_orig/Rhagoletis_zephyria/trackList.json b/organisms_orig/Rhagoletis_zephyria/trackList.json new file mode 100644 index 0000000..8dc9434 --- /dev/null +++ b/organisms_orig/Rhagoletis_zephyria/trackList.json @@ -0,0 +1,261 @@ +{ + "css" : "./plugins/NAL_CSS/css/contrib_styles.css", + "share_link" : 0, + "plugins" : [ + { + "location" : "./plugins/WebApollo", + "name" : "WebApollo" + } + ], + "tracks" : [ + { + "storeClass" : "JBrowse/Store/Sequence/StaticChunked", + "chunkSize" : 20000, + "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-", + "label" : "DNA", + "type" : "SequenceTrack", + "category" : "Reference sequence", + "key" : "Reference sequence" + }, + { + "autocomplete" : "none", + "style" : { + "className" : "annot", + "renderClassName" : "annot-render", + "subfeatureClasses" : { + "non_canonical_three_prime_splice_site" : "noncanonical-splice-site", + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "annot-CDS", + "non_canonical_five_prime_splice_site" : "noncanonical-splice-site", + "UTR" : "annot-UTR" + }, + "arrowheadClass" : "annot-arrowhead", + "alternateClasses" : { + "transposable_element" : { + "renderClassName" : "blue-ibeam-render", + "className" : "blue-ibeam" + }, + "pseudogene" : { + "renderClassName" : "gray-center-30pct", + "className" : "light-purple-80pct" + }, + "snRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "rRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "snoRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "repeat_region" : { + "className" : "magenta-80pct" + }, + "miRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "tRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "ncRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + } + }, + "uniqueIdField" : "id", + "centerSubFeature" : { + "non_canonical_three_prime_splice_site" : false, + "non_canonical_five_prime_splice_site" : false + } + }, + "key" : "User-created Annotations", + "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad", + "phase" : 0, + "compress" : 0, + "label" : "Annotations", + "type" : "WebApollo/View/Track/AnnotTrack", + "subfeatures" : 1 + }, + { + "style" : { + "pos_color" : "black", + "neg_color" : "white" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "key" : "Gaps in assembly", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/GCF_001687245.1_Rhagoletis_zephyria_1.0_genomic_RefSeqIDs.fna.gaps.bigwig", + "category" : "Reference Assembly", + "label" : "Gaps in assembly", + "type" : "JBrowse/View/Track/Wiggle/Density", + "metadata" : { + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank", + "Track contact" : "The i5k workspace@NAL" + } + }, + { + "style" : { + "neg_color" : "rgba(255,255,0,50)", + "pos_color" : "rgba(0,0,255,50)" + }, + "bicolor_pivot" : "0.5", + "key" : "GC Content", + "scoreType": "avgScore", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/GCF_001687245.1_Rhagoletis_zephyria_1.0_genomic_RefSeqIDs.fna.gc.bigwig", + "category" : "Reference Assembly", + "type" : "JBrowse/View/Track/Wiggle/Density", + "metadata" : { + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track contact" : "The i5k workspace@NAL" + }, + "label" : "GC Content" + }, + { + "style" : { + "className" : "container-16px", + "description": "product,note,description", + "subfeatureClasses" : { + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "gnomon_CDS", + "UTR" : "gnomon_UTR" + }, + "arrowheadClass" : "trellis-arrowhead" + }, + "key" : "NCBI Predicted lncRNA, Annotation Release 100", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/NCBI_Annotation_Release_100_lncRNA/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "metadata" : { + "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_001687245.1_Rhagoletis_zephyria_1.0/GCF_001687245.1_Rhagoletis_zephyria_1.0_genomic.gff.gz", + "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/", + "Data provider" : "NCBI", + "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Rhagoletis_zephyria/README_CURRENT_RELEASE" + }, + "label" : "NCBI_Annotation_Release_100_lncRNA", + "category" : "NCBI Annotation Release 100/1. Gene Sets/Noncoding" + }, + { + "style" : { + "className" : "container-16px", + "description": "product,note,description", + "subfeatureClasses" : { + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "gnomon_CDS", + "UTR" : "gnomon_UTR" + }, + "arrowheadClass" : "trellis-arrowhead" + }, + "key" : "NCBI Predicted pseudogenes, Annotation Release 100", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json", + "compress" : 0, + "label" : "NCBI_Annotation_Release_100_Pseudogene", + "category" : "NCBI Annotation Release 100/1. Gene Sets/Pseudogenes", + "metadata" : { + "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_001687245.1_Rhagoletis_zephyria_1.0/GCF_001687245.1_Rhagoletis_zephyria_1.0_genomic.gff.gz", + "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/", + "Data provider" : "NCBI", + "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Rhagoletis_zephyria/README_CURRENT_RELEASE" + }, + "type" : "FeatureTrack" + }, + { + "style" : { + "className" : "container-16px", + "description": "product,note,description", + "subfeatureClasses" : { + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "gnomon_CDS", + "UTR" : "gnomon_UTR" + }, + "arrowheadClass" : "trellis-arrowhead" + }, + "key" : "NCBI Predicted tRNAs, Annotation Release 100", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/NCBI_Annotation_Release_100_tRNA/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_001687245.1_Rhagoletis_zephyria_1.0/GCF_001687245.1_Rhagoletis_zephyria_1.0_genomic.gff.gz", + "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/", + "Data provider" : "NCBI", + "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Rhagoletis_zephyria/README_CURRENT_RELEASE" + }, + "type" : "FeatureTrack", + "category" : "NCBI Annotation Release 100/1. Gene Sets/Noncoding", + "label" : "NCBI_Annotation_Release_100_tRNA" + }, + { + "style" : { + "className" : "container-10px", + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "cDNA match evidence from NCBI Annotation Release 100", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/NCBI_Annotation_Release_100_cDNA_match/{refseq}/trackData.json", + "compress" : 0, + "category" : "NCBI Annotation Release 100/2. Evidence", + "label" : "NCBI_Annotation_Release_100_cDNA_match", + "type" : "FeatureTrack", + "metadata" : { + "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_001687245.1_Rhagoletis_zephyria_1.0/GCF_001687245.1_Rhagoletis_zephyria_1.0_genomic.gff.gz", + "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/", + "Data provider" : "NCBI", + "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Rhagoletis_zephyria/README_CURRENT_RELEASE" + } + }, + { + "style" : { + "className" : "container-16px", + "description": "product,note,description", + "subfeatureClasses" : { + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "primary_gene_set-cds", + "UTR" : "primary_gene_set-utr" + }, + "arrowheadClass" : "trellis-arrowhead" + }, + "key" : "NCBI Predicted protein coding genes, Annotation Release 100", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/rhazep_current_models/{refseq}/trackData.json", + "compress" : 0, + "label" : "rhazep_current_models", + "category" : "NCBI Annotation Release 100/1. Gene Sets/Protein Coding", + "metadata" : { + "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/", + "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_001687245.1_Rhagoletis_zephyria_1.0/GCF_001687245.1_Rhagoletis_zephyria_1.0_genomic.gff.gz", + "Data provider" : "NCBI", + "Note" : "Some genes may have non-coding transcripts", + "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Rhagoletis_zephyria/README_CURRENT_RELEASE" + }, + "type" : "FeatureTrack" + } + ], + "names" : { + "url" : "names/", + "type" : "Hash" + }, + "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico", + "alwaysOnTracks" : "DNA,Annotations", + "formatVersion" : 1 +} diff --git a/organisms_orig/Rhipicephalus_microplus/trackList.json b/organisms_orig/Rhipicephalus_microplus/trackList.json new file mode 100644 index 0000000..2c2ad7e --- /dev/null +++ b/organisms_orig/Rhipicephalus_microplus/trackList.json @@ -0,0 +1,128 @@ +{ + "css" : "./plugins/NAL_CSS/css/contrib_styles.css", + "share_link" : 0, + "plugins" : [ + { + "location" : "./plugins/WebApollo", + "name" : "WebApollo" + } + ], + "tracks" : [ + { + "storeClass" : "JBrowse/Store/Sequence/StaticChunked", + "chunkSize" : 20000, + "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-", + "label" : "DNA", + "type" : "SequenceTrack", + "category" : "Reference sequence", + "key" : "Reference sequence" + }, + { + "autocomplete" : "none", + "style" : { + "className" : "annot", + "renderClassName" : "annot-render", + "subfeatureClasses" : { + "non_canonical_three_prime_splice_site" : "noncanonical-splice-site", + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "annot-CDS", + "non_canonical_five_prime_splice_site" : "noncanonical-splice-site", + "UTR" : "annot-UTR" + }, + "arrowheadClass" : "annot-arrowhead", + "alternateClasses" : { + "transposable_element" : { + "renderClassName" : "blue-ibeam-render", + "className" : "blue-ibeam" + }, + "pseudogene" : { + "renderClassName" : "gray-center-30pct", + "className" : "light-purple-80pct" + }, + "snRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "rRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "snoRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "repeat_region" : { + "className" : "magenta-80pct" + }, + "ncRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "miRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + }, + "tRNA" : { + "renderClassName" : "gray-center-30pct", + "className" : "brightgreen-80pct" + } + }, + "uniqueIdField" : "id", + "centerSubFeature" : { + "non_canonical_three_prime_splice_site" : false, + "non_canonical_five_prime_splice_site" : false + } + }, + "key" : "User-created Annotations", + "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad", + "phase" : 0, + "compress" : 0, + "label" : "Annotations", + "type" : "WebApollo/View/Track/AnnotTrack", + "subfeatures" : 1 + }, + { + "style" : { + "pos_color" : "black", + "neg_color" : "white" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "key" : "Gaps in assembly", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/GCA_002176555.1_Rmi2.0_genomic.fna.gaps.bigwig", + "label" : "Gaps in assembly", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track contact" : "The i5k workspace@NAL" + }, + "type" : "JBrowse/View/Track/Wiggle/Density" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/GCA_002176555.1_Rmi2.0_genomic.fna.gc.bigwig", + "style" : { + "neg_color" : "rgba(255,255,0,50)", + "pos_color" : "rgba(0,0,255,50)" + }, + "label" : "GC Content", + "type" : "JBrowse/View/Track/Wiggle/Density", + "bicolor_pivot" : "0.5", + "key" : "GC Content", + "scoreType": "avgScore", + "category" : "Reference Assembly", + "metadata" : { + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track contact" : "The i5k workspace@NAL" + }, + "autoscale" : "local" + } + ], + "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico", + "alwaysOnTracks" : "DNA,Annotations", + "formatVersion" : 1 +} diff --git a/organisms_orig/Rhyzopertha_dominica/trackList.json b/organisms_orig/Rhyzopertha_dominica/trackList.json new file mode 100644 index 0000000..b304273 --- /dev/null +++ b/organisms_orig/Rhyzopertha_dominica/trackList.json @@ -0,0 +1,423 @@ +{ + "formatVersion" : 1, + "names" : { + "type" : "Hash", + "url" : "names/" + }, + "tracks" : [ + { + "category" : "Reference sequence", + "chunkSize" : 20000, + "key" : "Reference sequence", + "label" : "DNA", + "seqType" : "dna", + "storeClass" : "JBrowse/Store/Sequence/StaticChunked", + "type" : "SequenceTrack", + "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Reference Assembly", + "key" : "Gaps in assembly", + "label" : "Gaps in assembly", + "metadata" : { + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "neg_color" : "white", + "pos_color" : "black" + }, + "type" : "JBrowse/View/Track/Wiggle/Density", + "urlTemplate" : "bigwig/_____RdoDt3_Drdd8_decomES.fasta.gaps.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "0.5", + "category" : "Reference Assembly", + "key" : "GC Content", + "label" : "GC Content", + "metadata" : { + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "neg_color" : "rgba(255,255,0,50)", + "pos_color" : "rgba(0,0,255,50)" + }, + "type" : "JBrowse/View/Track/Wiggle/Density", + "urlTemplate" : "bigwig/_____RdoDt3_Drdd8_decomES.fasta.gc.bigwig" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "Gut3", + "label" : "Gut3", + "metadata" : { + "Analysis provider" : "Brenda Oppert, USDA-ARS", + "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand
Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
Yellow marking - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "analyses/Rhyzopertha-dominica-RNA-Seq_05-2020/Gut3.sorted.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "RNA-Seq/Coverage Plots", + "key" : "Gut3, coverage", + "label" : "Gut3, coverage", + "metadata" : { + "Analysis provider" : "Brenda Oppert, USDA-ARS", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "analyses/Rhyzopertha-dominica-RNA-Seq_05-2020/Gut3.sorted.bigwig" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "Adult", + "label" : "Adult", + "metadata" : { + "Analysis provider" : "Brenda Oppert, USDA-ARS", + "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand
Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
Yellow marking - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "analyses/Rhyzopertha-dominica-RNA-Seq_05-2020/Adult.sorted.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "RNA-Seq/Coverage Plots", + "key" : "Adult, coverage", + "label" : "Adult, coverage", + "metadata" : { + "Analysis provider" : "Brenda Oppert, USDA-ARS", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "analyses/Rhyzopertha-dominica-RNA-Seq_05-2020/Adult.sorted.bigwig" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "Head2", + "label" : "Head2", + "metadata" : { + "Analysis provider" : "Brenda Oppert, USDA-ARS", + "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand
Light red alignments: Spliced portion of read aligned to forward strand
Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
Yellow marking - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "analyses/Rhyzopertha-dominica-RNA-Seq_05-2020/Head2.sorted.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "RNA-Seq/Coverage Plots", + "key" : "Head2, coverage", + "label" : "Head2, coverage", + "metadata" : { + "Analysis provider" : "Brenda Oppert, USDA-ARS", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "analyses/Rhyzopertha-dominica-RNA-Seq_05-2020/Head2.sorted.bigwig" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "Carcass1", + "label" : "Carcass1", + "metadata" : { + "Analysis provider" : "Brenda Oppert, USDA-ARS", + "Track legend" : "Dark red alignments: Mapped portion of read aligned to forward strand
Light red alignments: Spliced portion of read aligned to forward strand
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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "repeatmasker", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatmasker" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "repeatrunner", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatrunner" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "snap" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/1. 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Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", +}, + "key" : "GC Content", + "scoreType": "avgScore", + + + "autoscale" : "local" + } + ], + "names" : { + "url" : "names/", + "type" : "Hash" + }, + "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico", + "alwaysOnTracks" : "DNA,Annotations", + "formatVersion" : 1 +} diff --git a/organisms_orig/Varroa_destructor/trackList.json b/organisms_orig/Varroa_destructor/trackList.json new file mode 100644 index 0000000..52ffaed --- /dev/null +++ b/organisms_orig/Varroa_destructor/trackList.json @@ -0,0 +1,112 @@ +{ + "formatVersion" : 1, + "names" : { + "type" : "Hash", + "url" : "names/" + }, + "tracks" : [ + { + "category" : "Reference sequence", + "faiUrlTemplate" : "seq/GCF_002443255.1_Vdes_3.0_genomic.fna.fai", + "key" : "Reference sequence", + "label" : "DNA", + "seqType" : "dna", + "storeClass" : "JBrowse/Store/Sequence/IndexedFasta", + "type" : "SequenceTrack", + "urlTemplate" : "seq/GCF_002443255.1_Vdes_3.0_genomic.fna", + "useAsRefSeqStore" : 1 + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Reference Assembly", + "key" : "Gaps in assembly", + "label" : "Gaps in assembly", + "metadata" : { + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track legend" : "Visualization of gaps in the reference assembly. 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The pivot point is 0.5, or 50% G+C or A+T. 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"NCBI_Annotation_Release_100_Pseudogene", + "label" : "NCBI_Annotation_Release_100_Pseudogene", + "metadata" : { + "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use", + "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Varroa_jacobsoni/README_CURRENT_RELEASE", + "Data provider" : "NCBI", + "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/532/875/GCF_002532875.1_vjacob_1.0/GCF_002532875.1_vjacob_1.0_genomic.gff.gz", + "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/" + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "trellis-arrowhead", + "className" : "container-16px", + "description" : "product, note, description", + "subfeatureClasses" : { + "CDS" : "gnomon_CDS", + "UTR" : "gnomon_UTR", + "exon" : "container-100pct", + "wholeCDS" : null + } + }, + "trackType" : "HTMLFeatures", + "type" : "HTMLFeatures", + "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json" + } + ] +} diff --git a/organisms_orig/command_file.sh b/organisms_orig/command_file.sh new file mode 100644 index 0000000..ff9699d --- /dev/null +++ b/organisms_orig/command_file.sh @@ -0,0 +1,125 @@ +mkdir Aethina_tumida; cd Aethina_tumida; cp /app/data/other_species/aettum/jbrowse/data/trackList.json .; cd .. +mkdir Agrilus_planipennis; cd Agrilus_planipennis; cp /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/trackList.json .; cd .. +mkdir Amyelois_transitella; cd Amyelois_transitella; cp /app/data/other_species/amytra/jbrowse/data/trackList.json .; cd .. +mkdir Anoplophora_glabripennis; cd Anoplophora_glabripennis; cp /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Apis_mellifera; cd Apis_mellifera; cp /app/data/other_species/apimel/Amel_4.5/jbrowse/data//trackList.json .; cd .. +mkdir Athalia_rosae; cd Athalia_rosae; cp /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Bactrocera_cucurbitae; cd Bactrocera_cucurbitae; cp /app/data/other_species/baccuc/jbrowse/data/trackList.json .; cd .. +mkdir Bactrocera_dorsalis; cd Bactrocera_dorsalis; cp /app/data/other_species/bacdor/jbrowse/data/trackList.json .; cd .. +mkdir Bactrocera_oleae; cd Bactrocera_oleae; cp /app/data/other_species/bacole/jbrowse/data/trackList.json .; cd .. +mkdir Bemisia_tabaci; cd Bemisia_tabaci; cp /app/data/other_species/bemtab/jbrowse/data/trackList.json .; cd .. +mkdir Blattella_germanica; cd Blattella_germanica; cp /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Bombus_terrestris; cd Bombus_terrestris; cp /app/data/other_species/bomter/Bter_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Bombus_impatiens; cd Bombus_impatiens; cp /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data/trackList.json .; cd .. +mkdir Catajapyx_aquilonaris; cd Catajapyx_aquilonaris; cp /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/trackList.json .; cd .. +mkdir Centruroides_sculpturatus; cd Centruroides_sculpturatus; cp /app/data/BCM_i5k_pilot/censcu/jbrowse/data/trackList.json .; cd .. +mkdir Cephus_cinctus; cd Cephus_cinctus; cp /app/data/other_species/cepcin/Ccin1/jbrowse/data//trackList.json .; cd .. +mkdir Ceratitis_capitata; cd Ceratitis_capitata; cp /app/data/BCM_i5k_pilot/cercap/jbrowse/data/trackList.json .; cd .. +mkdir Chelonus_insularis; cd Chelonus_insularis; cp /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/trackList.json .; cd .. +mkdir Cimex_lectularius; cd Cimex_lectularius; cp /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Clitarchus_hookeri; cd Clitarchus_hookeri; cp /app/data/other_species/clihoo/jbrowse/data/trackList.json .; cd .. +mkdir Contarinia_nasturtii; cd Contarinia_nasturtii; cp /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/trackList.json .; cd .. +mkdir Copidosoma_floridanum; cd Copidosoma_floridanum; cp /app/data/BCM_i5k_pilot/copflo/jbrowse/data/trackList.json .; cd .. +mkdir Diachasma_alloeum; cd Diachasma_alloeum; cp /app/data/other_species/diaall/Dall2.0/jbrowse/data/trackList.json .; cd .. +mkdir Diaphorina_citri; cd Diaphorina_citri; cp /app/data/other_species/diacit/jbrowse/data/trackList.json .; cd .. +mkdir Diaphorina_citri_legacy; cd Diaphorina_citri_legacy; cp /app/data/other_species/diacit_legacy/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_ficusphila; cd Drosophila_ficusphila; cp /app/data/modencode/drofic/Dfic_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_elegans; cd Drosophila_elegans; cp /app/data/modencode/droele/Dele_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_bipectinata; cd Drosophila_bipectinata; cp /app/data/modencode/drobip/Dbip_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_biarmipes; cd Drosophila_biarmipes; cp /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_eugracilis; cd Drosophila_eugracilis; cp /app/data/modencode/droeug/Deug_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_takahashii; cd Drosophila_takahashii; cp /app/data/modencode/drotak/Dtak_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_rhopaloa; cd Drosophila_rhopaloa; cp /app/data/modencode/drorho/Drho_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_kikkawai; cd Drosophila_kikkawai; cp /app/data/modencode/drokik/Dkik_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Dufourea_novaeangliae; cd Dufourea_novaeangliae; cp /app/data/other_species/dufnov/jbrowse/data/trackList.json .; cd .. +mkdir Ephemera_danica; cd Ephemera_danica; cp /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data//trackList.json .; cd .. +mkdir Eufriesea_mexicana; cd Eufriesea_mexicana; cp /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/trackList.json .; cd .. +mkdir Euglossa_dilemma; cd Euglossa_dilemma; cp /app/data/other_species/eugdil/jbrowse/data/trackList.json .; cd .. +mkdir Eurytemora_affinis_-_training; cd Eurytemora_affinis_-_training; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. +mkdir Eurytemora_affinis; cd Eurytemora_affinis; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. +mkdir Fopius_arisanus; cd Fopius_arisanus; cp /app/data/other_species/fopari/jbrowse/data/trackList.json .; cd .. +mkdir Frankliniella_occidentalis; cd Frankliniella_occidentalis; cp /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/trackList.json .; cd .. +mkdir Galleria_mellonella; cd Galleria_mellonella; cp /app/data/other_species/galmel/ASM364042v2/jbrowse/data/trackList.json .; cd .. +mkdir Gerris_buenoi; cd Gerris_buenoi; cp /app/data/BCM_i5k_pilot/gerbue/jbrowse/data//trackList.json .; cd .. +mkdir Habropoda_laboriosa; cd Habropoda_laboriosa; cp /app/data/other_species/hablab/jbrowse/data/trackList.json .; cd .. +mkdir Halyomorpha_halys; cd Halyomorpha_halys; cp /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/trackList.json .; cd .. +mkdir Heliothis_virescens; cd Heliothis_virescens; cp /app/data/other_species/helvir/jbrowse/data//trackList.json .; cd .. +mkdir Holacanthella_duospinosa; cd Holacanthella_duospinosa; cp /app/data/other_species/holduo/ASM273828v1/jbrowse/data/trackList.json .; cd .. +mkdir Homalodisca_vitripennis; cd Homalodisca_vitripennis; cp /app/data/BCM_i5k_pilot/homvit/jbrowse/data/trackList.json .; cd .. +mkdir Hyalella_azteca; cd Hyalella_azteca; cp /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/trackList.json .; cd .. +mkdir Ladona_fulva; cd Ladona_fulva; cp /app/data/BCM_i5k_pilot/ladful/jbrowse/data/trackList.json .; cd .. +mkdir Laodelphax_striatellus; cd Laodelphax_striatellus; cp /app/data/other_species/laostr/ASM333518v2/jbrowse/data/trackList.json .; cd .. +mkdir Lasioglossum_albipes; cd Lasioglossum_albipes; cp /app/data/other_species/lasalb/jbrowse/data/trackList.json .; cd .. +mkdir Latrodectus_hesperus; cd Latrodectus_hesperus; cp /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/trackList.json .; cd .. +mkdir Leptinotarsa_decemlineata_training; cd Leptinotarsa_decemlineata_training; cp /app/data/BCM_i5k_pilot/lepdec/jbrowse/data/trackList.json .; cd .. +mkdir Leptinotarsa_decemlineata; cd Leptinotarsa_decemlineata; cp /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Limnephilus_lunatus; cd Limnephilus_lunatus; cp /app/data/BCM_i5k_pilot/limlun/jbrowse/data/trackList.json .; cd .. +mkdir Locusta_migratoria; cd Locusta_migratoria; cp /app/data/other_species/locmig/jbrowse/data//trackList.json .; cd .. +mkdir Loxosceles_reclusa; cd Loxosceles_reclusa; cp /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data/trackList.json .; cd .. +mkdir Manduca_sexta; cd Manduca_sexta; cp /app/data/other_species/mansex/jbrowse/data/trackList.json .; cd .. +mkdir Mayetiola_destructor; cd Mayetiola_destructor; cp /app/data/other_species/maydes/jbrowse/data/trackList.json .; cd .. +mkdir Medauroidea_extradentata; cd Medauroidea_extradentata; cp /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/trackList.json .; cd .. +mkdir Megachile_rotundata; cd Megachile_rotundata; cp /app/data/other_species/megrot/jbrowse/data/trackList.json .; cd .. +mkdir Melipona_quadrifasciata; cd Melipona_quadrifasciata; cp /app/data/other_species/melqua/jbrowse/data/trackList.json .; cd .. +mkdir Microplitis_demolitor; cd Microplitis_demolitor; cp /app/data/other_species/micdem/jbrowse/data/trackList.json .; cd .. +mkdir Neodiprion_lecontei_training; cd Neodiprion_lecontei_training; cp /app/data/other_species/neolec/jbrowse/data/trackList.json .; cd .. +mkdir Neodiprion_lecontei; cd Neodiprion_lecontei; cp /app/data/other_species/neolec/Nlec1.1/jbrowse/data/trackList.json .; cd .. +mkdir Nicrophorus_vespilloides; cd Nicrophorus_vespilloides; cp /app/data/other_species/nicves/jbrowse/data/trackList.json .; cd .. +mkdir Nylanderia_fulva; cd Nylanderia_fulva; cp /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Odontomachus_brunneus; cd Odontomachus_brunneus; cp /app/data/other_species/odobru/Obru_v1/jbrowse/data/trackList.json .; cd .. +mkdir Oncopeltus_fasciatus; cd Oncopeltus_fasciatus; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. +mkdir Oncopeltus_fasciatus_training; cd Oncopeltus_fasciatus_training; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. +mkdir 33_-_Onthophagus_taurus_training; cd 33_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 2_-_Onthophagus_taurus_training; cd 2_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 10_-_Onthophagus_taurus_training; cd 10_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 39_-_Onthophagus_taurus_training; cd 39_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 31_-_Onthophagus_taurus_training; cd 31_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 35_-_Onthophagus_taurus_training; cd 35_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 40_-_Onthophagus_taurus_training; cd 40_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 36_-_Onthophagus_taurus_training; cd 36_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 37_-_Onthophagus_taurus_training; cd 37_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 18_-_Onthophagus_taurus_training; cd 18_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 19_-_Onthophagus_taurus_training; cd 19_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 20_-_Onthophagus_taurus_training; cd 20_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 22_-_Onthophagus_taurus_training; cd 22_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 25_-_Onthophagus_taurus_training; cd 25_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 38_-_Onthophagus_taurus_training; cd 38_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 7_-_Onthophagus_taurus_training; cd 7_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 3_-_Onthophagus_taurus_training; cd 3_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 4_-_Onthophagus_taurus_training; cd 4_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir Onthophagus_taurus; cd Onthophagus_taurus; cp /app/data/BCM_i5k_pilot/onttau/jbrowse/data/trackList.json .; cd .. +mkdir 8_-_Onthophagus_taurus_training; cd 8_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 5_-_Onthophagus_taurus_training; cd 5_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 6_-_Onthophagus_taurus_training; cd 6_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 9_-_Onthophagus_taurus_training; cd 9_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 13_-_Onthophagus_taurus_training; cd 13_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 12_-_Onthophagus_taurus_training; cd 12_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 15_-_Onthophagus_taurus_training; cd 15_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 14_-_Onthophagus_taurus_training; cd 14_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 16_-_Onthophagus_taurus_training; cd 16_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 17_-_Onthophagus_taurus_training; cd 17_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 1_-_Onthophagus_taurus_training; cd 1_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 11_-_Onthophagus_taurus_training; cd 11_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 32_-_Onthophagus_taurus_training; cd 32_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 21_-_Onthophagus_taurus_training; cd 21_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 23_-_Onthophagus_taurus_training; cd 23_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 24_-_Onthophagus_taurus_training; cd 24_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 26_-_Onthophagus_taurus_training; cd 26_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 27_-_Onthophagus_taurus_training; cd 27_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 28_-_Onthophagus_taurus_training; cd 28_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 34_-_Onthophagus_taurus_training; cd 34_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 29_-_Onthophagus_taurus_training; cd 29_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 30_-_Onthophagus_taurus_training; cd 30_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir Orussus_abietinus; cd Orussus_abietinus; cp /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Osmia_lignaria; cd Osmia_lignaria; cp /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Pachypsylla_venusta; cd Pachypsylla_venusta; cp /app/data/BCM_i5k_pilot/pacven/jbrowse/data/trackList.json .; cd .. +mkdir Parasteatoda_tepidariorum; cd Parasteatoda_tepidariorum; cp /app/data/BCM_i5k_pilot/partep/jbrowse/data/trackList.json .; cd .. +mkdir Rhagoletis_zephyria; cd Rhagoletis_zephyria; cp /app/data/other_species/rhazep/jbrowse/data/trackList.json .; cd .. +mkdir Rhipicephalus_microplus; cd Rhipicephalus_microplus; cp /app/data/other_species/rhimic/jbrowse/data/trackList.json .; cd .. +mkdir Rhyzopertha_dominica; cd Rhyzopertha_dominica; cp /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/trackList.json .; cd .. +mkdir Tigriopus_californicus; cd Tigriopus_californicus; cp /app/data/other_species/tigcal/jbrowse/data/trackList.json .; cd .. +mkdir Tribolium_castaneum; cd Tribolium_castaneum; cp /app/data/other_species/tricas/jbrowse/data/trackList.json .; cd .. +mkdir Trichogramma_pretiosum; cd Trichogramma_pretiosum; cp /app/data/BCM_i5k_pilot/tripre/jbrowse/data/trackList.json .; cd .. +mkdir Varroa_jacobsoni; cd Varroa_jacobsoni; cp /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Varroa_destructor; cd Varroa_destructor; cp /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/trackList.json .; cd .. +mkdir Mamestra_configurata; cd Mamestra_configurata; cp /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/trackList.json .; cd .. diff --git a/organisms_orig/directory_list.orig b/organisms_orig/directory_list.orig new file mode 100644 index 0000000..cb20ddd --- /dev/null +++ b/organisms_orig/directory_list.orig @@ -0,0 +1,129 @@ +webapollo_2=# select common_name, directory from organism ORDER BY genus; + common_name | directory +------------------------------------+------------------------------------------------------------- + Aethina_tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus_planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois_transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora_glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis_mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia_rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera_cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera_dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera_oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia_tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella_germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus_terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Bombus_impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Catajapyx_aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides_sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus_cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis_capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus_insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex_lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus_hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia_nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma_floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma_alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina_citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina_citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila_ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila_elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila_bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila_biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila_eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila_takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Drosophila_rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila_kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Dufourea_novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera_danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea_mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa_dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora_affinis_-_training | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora_affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius_arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella_occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria_mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris_buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda_laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha_halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis_virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella_duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca_vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella_azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona_fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax_striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum_albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus_hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa_decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Leptinotarsa_decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Limnephilus_lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta_migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles_reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Manduca_sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola_destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea_extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile_rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona_quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis_demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion_lecontei_training | /app/data/other_species/neolec/jbrowse/data + Neodiprion_lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Nicrophorus_vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia_fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus_brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus_fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus_fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + 33_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 2_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 10_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 39_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 31_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 35_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 40_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 36_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 37_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 18_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 19_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 20_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 22_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 25_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 38_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 7_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 3_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 4_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + Onthophagus_taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + 8_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 5_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 6_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 9_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 13_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 12_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 15_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 14_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 16_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 17_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 1_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 11_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 32_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 21_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 23_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 24_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 26_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 27_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 28_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 34_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 29_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 30_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + Orussus_abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia_lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla_venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda_tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis_zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus_microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha_dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Tigriopus_californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium_castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma_pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa_jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data + Varroa_destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Mamestra_configurata | /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data +(125 rows) diff --git a/organisms_orig/directory_list.orig.sorted b/organisms_orig/directory_list.orig.sorted new file mode 100644 index 0000000..01a3504 --- /dev/null +++ b/organisms_orig/directory_list.orig.sorted @@ -0,0 +1,129 @@ +------------------------------------+------------------------------------------------------------- + 10_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 11_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +(125 rows) + 12_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 13_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 14_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 15_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 16_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 17_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 18_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 19_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 1_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 20_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 21_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 22_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 23_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 24_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 25_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 26_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 27_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 28_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 29_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 2_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 30_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 31_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 32_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 33_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 34_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 35_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 36_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 37_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 38_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 39_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 3_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 40_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 4_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 5_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 6_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 7_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 8_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 9_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + Aethina_tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus_planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois_transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora_glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis_mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia_rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera_cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera_dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera_oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia_tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella_germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus_impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Bombus_terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Catajapyx_aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides_sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus_cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis_capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus_insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex_lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus_hookeri | /app/data/other_species/clihoo/jbrowse/data + common_name | directory + Contarinia_nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma_floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma_alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina_citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina_citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila_biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila_bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila_elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila_eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila_ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila_kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Drosophila_rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila_takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Dufourea_novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera_danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea_mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa_dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora_affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora_affinis_-_training | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius_arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella_occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria_mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris_buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda_laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha_halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis_virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella_duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca_vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella_azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona_fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax_striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum_albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus_hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa_decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Leptinotarsa_decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Limnephilus_lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta_migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles_reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Mamestra_configurata | /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data + Manduca_sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola_destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea_extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile_rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona_quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis_demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion_lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Neodiprion_lecontei_training | /app/data/other_species/neolec/jbrowse/data + Nicrophorus_vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia_fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus_brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus_fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus_fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Onthophagus_taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + Orussus_abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia_lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla_venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda_tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis_zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus_microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha_dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Tigriopus_californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium_castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma_pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa_destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Varroa_jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data +webapollo_2=# select common_name, directory from organism ORDER BY genus; diff --git a/organisms_orig/directory_list.txt b/organisms_orig/directory_list.txt new file mode 100644 index 0000000..710b05f --- /dev/null +++ b/organisms_orig/directory_list.txt @@ -0,0 +1,125 @@ +Aethina_tumida|/app/data/other_species/aettum/jbrowse/data +Agrilus_planipennis|/app/data/BCM_i5k_pilot/agrpla/jbrowse/data +Amyelois_transitella|/app/data/other_species/amytra/jbrowse/data +Anoplophora_glabripennis|/app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data +Apis_mellifera|/app/data/other_species/apimel/Amel_4.5/jbrowse/data/ +Athalia_rosae|/app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data +Bactrocera_cucurbitae|/app/data/other_species/baccuc/jbrowse/data +Bactrocera_dorsalis|/app/data/other_species/bacdor/jbrowse/data +Bactrocera_oleae|/app/data/other_species/bacole/jbrowse/data +Bemisia_tabaci|/app/data/other_species/bemtab/jbrowse/data +Blattella_germanica|/app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data +Bombus_terrestris|/app/data/other_species/bomter/Bter_1.0/jbrowse/data +Bombus_impatiens|/app/data/other_species/bomimp/BIMP_2.1/jbrowse/data +Catajapyx_aquilonaris|/app/data/BCM_i5k_pilot/cataqu/jbrowse/data +Centruroides_sculpturatus|/app/data/BCM_i5k_pilot/censcu/jbrowse/data +Cephus_cinctus|/app/data/other_species/cepcin/Ccin1/jbrowse/data/ +Ceratitis_capitata|/app/data/BCM_i5k_pilot/cercap/jbrowse/data +Chelonus_insularis|/app/data/other_species/cheins/ASM1335770v1/jbrowse/data +Cimex_lectularius|/app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data +Clitarchus_hookeri|/app/data/other_species/clihoo/jbrowse/data +Contarinia_nasturtii|/app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data +Copidosoma_floridanum|/app/data/BCM_i5k_pilot/copflo/jbrowse/data +Diachasma_alloeum|/app/data/other_species/diaall/Dall2.0/jbrowse/data +Diaphorina_citri|/app/data/other_species/diacit/jbrowse/data +Diaphorina_citri_legacy|/app/data/other_species/diacit_legacy/jbrowse/data +Drosophila_ficusphila|/app/data/modencode/drofic/Dfic_2.0/jbrowse/data +Drosophila_elegans|/app/data/modencode/droele/Dele_2.0/jbrowse/data +Drosophila_bipectinata|/app/data/modencode/drobip/Dbip_2.0/jbrowse/data +Drosophila_biarmipes|/app/data/modencode/drobia/Dbia_2.0/jbrowse/data +Drosophila_eugracilis|/app/data/modencode/droeug/Deug_2.0/jbrowse/data +Drosophila_takahashii|/app/data/modencode/drotak/Dtak_2.0/jbrowse/data +Drosophila_rhopaloa|/app/data/modencode/drorho/Drho_2.0/jbrowse/data +Drosophila_kikkawai|/app/data/modencode/drokik/Dkik_2.0/jbrowse/data +Dufourea_novaeangliae|/app/data/other_species/dufnov/jbrowse/data +Ephemera_danica|/app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ +Eufriesea_mexicana|/app/data/other_species/eufmex/ASM148370v1/jbrowse/data +Euglossa_dilemma|/app/data/other_species/eugdil/jbrowse/data +Eurytemora_affinis_-_training|/app/data/BCM_i5k_pilot/euraff/jbrowse/data +Eurytemora_affinis|/app/data/BCM_i5k_pilot/euraff/jbrowse/data +Fopius_arisanus|/app/data/other_species/fopari/jbrowse/data +Frankliniella_occidentalis|/app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data +Galleria_mellonella|/app/data/other_species/galmel/ASM364042v2/jbrowse/data +Gerris_buenoi|/app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ +Habropoda_laboriosa|/app/data/other_species/hablab/jbrowse/data +Halyomorpha_halys|/app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data +Heliothis_virescens|/app/data/other_species/helvir/jbrowse/data/ +Holacanthella_duospinosa|/app/data/other_species/holduo/ASM273828v1/jbrowse/data +Homalodisca_vitripennis|/app/data/BCM_i5k_pilot/homvit/jbrowse/data +Hyalella_azteca|/app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data +Ladona_fulva|/app/data/BCM_i5k_pilot/ladful/jbrowse/data +Laodelphax_striatellus|/app/data/other_species/laostr/ASM333518v2/jbrowse/data +Lasioglossum_albipes|/app/data/other_species/lasalb/jbrowse/data +Latrodectus_hesperus|/app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data +Leptinotarsa_decemlineata_training|/app/data/BCM_i5k_pilot/lepdec/jbrowse/data +Leptinotarsa_decemlineata|/app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data +Limnephilus_lunatus|/app/data/BCM_i5k_pilot/limlun/jbrowse/data +Locusta_migratoria|/app/data/other_species/locmig/jbrowse/data/ +Loxosceles_reclusa|/app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data +Manduca_sexta|/app/data/other_species/mansex/jbrowse/data +Mayetiola_destructor|/app/data/other_species/maydes/jbrowse/data +Medauroidea_extradentata|/app/data/other_species/medext/GCA_003012365.1/jbrowse/data +Megachile_rotundata|/app/data/other_species/megrot/jbrowse/data +Melipona_quadrifasciata|/app/data/other_species/melqua/jbrowse/data +Microplitis_demolitor|/app/data/other_species/micdem/jbrowse/data +Neodiprion_lecontei_training|/app/data/other_species/neolec/jbrowse/data +Neodiprion_lecontei|/app/data/other_species/neolec/Nlec1.1/jbrowse/data +Nicrophorus_vespilloides|/app/data/other_species/nicves/jbrowse/data +Nylanderia_fulva|/app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data +Odontomachus_brunneus|/app/data/other_species/odobru/Obru_v1/jbrowse/data +Oncopeltus_fasciatus|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data +Oncopeltus_fasciatus_training|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data +33_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +2_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +10_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +39_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +31_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +35_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +40_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +36_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +37_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +18_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +19_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +20_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +22_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +25_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +38_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +7_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +3_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +4_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +Onthophagus_taurus|/app/data/BCM_i5k_pilot/onttau/jbrowse/data +8_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +5_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +6_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +9_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +13_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +12_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +15_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +14_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +16_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +17_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +1_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +11_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +32_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +21_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +23_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +24_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +26_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +27_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +28_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +34_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +29_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +30_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +Orussus_abietinus|/app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data +Osmia_lignaria|/app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data +Pachypsylla_venusta|/app/data/BCM_i5k_pilot/pacven/jbrowse/data +Parasteatoda_tepidariorum|/app/data/BCM_i5k_pilot/partep/jbrowse/data +Rhagoletis_zephyria|/app/data/other_species/rhazep/jbrowse/data +Rhipicephalus_microplus|/app/data/other_species/rhimic/jbrowse/data +Rhyzopertha_dominica|/app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data +Tigriopus_californicus|/app/data/other_species/tigcal/jbrowse/data +Tribolium_castaneum|/app/data/other_species/tricas/jbrowse/data +Trichogramma_pretiosum|/app/data/BCM_i5k_pilot/tripre/jbrowse/data +Varroa_jacobsoni|/app/data/other_species/varjac/vjacob_1.0/jbrowse/data +Varroa_destructor|/app/data/other_species/vardes/Vdes_3.0/jbrowse/data +Mamestra_configurata|/app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data diff --git a/organisms_orig/make_dir_script.pl b/organisms_orig/make_dir_script.pl new file mode 100644 index 0000000..5b2aa5f --- /dev/null +++ b/organisms_orig/make_dir_script.pl @@ -0,0 +1,9 @@ +#!/usr/bin/perl -w + +use strict; + +while (<>){ + $_ =~ m/(\S*)\|(\S*)/; + print "mkdir $1; cd $1; cp $2/trackList.json .; cd .. \n"; +} + diff --git a/organisms_orig/make_links.sh b/organisms_orig/make_links.sh new file mode 100644 index 0000000..e4e5b78 --- /dev/null +++ b/organisms_orig/make_links.sh @@ -0,0 +1,250 @@ +cp /app/data/other_species/aettum/jbrowse/data/trackList.json Aethina_tumida/ +cp /app/data/other_species/aettum/jbrowse/data/tracks.conf Aethina_tumida/ +cp /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/trackList.json Agrilus_planipennis/ +cp /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/tracks.conf Agrilus_planipennis/ +cp /app/data/other_species/amytra/jbrowse/data/trackList.json Amyelois_transitella/ +cp /app/data/other_species/amytra/jbrowse/data/tracks.conf Amyelois_transitella/ +cp /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/trackList.json Anoplophora_glabripennis/ +cp /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/tracks.conf Anoplophora_glabripennis/ +cp /app/data/other_species/apimel/Amel_4.5/jbrowse/data//trackList.json Apis_mellifera/ +cp /app/data/other_species/apimel/Amel_4.5/jbrowse/data//tracks.conf Apis_mellifera/ +cp /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/trackList.json Athalia_rosae/ +cp /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/tracks.conf Athalia_rosae/ +cp /app/data/other_species/baccuc/jbrowse/data/trackList.json Bactrocera_cucurbitae/ +cp /app/data/other_species/baccuc/jbrowse/data/tracks.conf Bactrocera_cucurbitae/ +cp /app/data/other_species/bacdor/jbrowse/data/trackList.json Bactrocera_dorsalis/ +cp /app/data/other_species/bacdor/jbrowse/data/tracks.conf Bactrocera_dorsalis/ +cp /app/data/other_species/bacole/jbrowse/data/trackList.json Bactrocera_oleae/ +cp /app/data/other_species/bacole/jbrowse/data/tracks.conf Bactrocera_oleae/ +cp /app/data/other_species/bemtab/jbrowse/data//trackList.json Bemisia_tabaci/ +cp /app/data/other_species/bemtab/jbrowse/data//tracks.conf Bemisia_tabaci/ +cp /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/trackList.json Blattella_germanica/ +cp /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/tracks.conf Blattella_germanica/ +cp /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data//trackList.json Bombus_impatiens/ +cp /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data//tracks.conf Bombus_impatiens/ +cp /app/data/other_species/bomter/Bter_1.0/jbrowse/data//trackList.json Bombus_terrestris/ +cp /app/data/other_species/bomter/Bter_1.0/jbrowse/data//tracks.conf Bombus_terrestris/ +cp /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/trackList.json Catajapyx_aquilonaris/ +cp /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/tracks.conf Catajapyx_aquilonaris/ +cp /app/data/BCM_i5k_pilot/censcu/Cexi_2.0/jbrowse/data//trackList.json Centruroides_sculpturatus/ +cp /app/data/BCM_i5k_pilot/censcu/Cexi_2.0/jbrowse/data//tracks.conf Centruroides_sculpturatus/ +cp /app/data/other_species/cepcin/Ccin1/jbrowse/data//trackList.json Cephus_cinctus/ +cp /app/data/other_species/cepcin/Ccin1/jbrowse/data//tracks.conf Cephus_cinctus/ +cp /app/data/BCM_i5k_pilot/cercap/jbrowse/data/trackList.json Ceratitis_capitata/ +cp /app/data/BCM_i5k_pilot/cercap/jbrowse/data/tracks.conf Ceratitis_capitata/ +cp /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/trackList.json Chelonus_insularis/ +cp /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/tracks.conf Chelonus_insularis/ +cp /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/trackList.json Cimex_lectularius/ +cp /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/tracks.conf Cimex_lectularius/ +cp /app/data/other_species/clihoo/jbrowse/data/trackList.json Clitarchus_hookeri/ +cp /app/data/other_species/clihoo/jbrowse/data/tracks.conf Clitarchus_hookeri/ +cp /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/trackList.json Contarinia_nasturtii/ +cp /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/tracks.conf Contarinia_nasturtii/ +cp /app/data/BCM_i5k_pilot/copflo/Cflo_2.0/jbrowse/data/trackList.json Copidosoma_floridanum/ +cp /app/data/BCM_i5k_pilot/copflo/Cflo_2.0/jbrowse/data/tracks.conf Copidosoma_floridanum/ +cp /app/data/other_species/diaall/Dall2.0/jbrowse/data/trackList.json Diachasma_alloeum/ +cp /app/data/other_species/diaall/Dall2.0/jbrowse/data/tracks.conf Diachasma_alloeum/ +cp /app/data/other_species/diacit/jbrowse/data/trackList.json Diaphorina_citri/ +cp /app/data/other_species/diacit/jbrowse/data/tracks.conf Diaphorina_citri/ +cp /app/data/other_species/diacit_legacy/jbrowse/data/trackList.json Diaphorina_citri_legacy/ +cp /app/data/other_species/diacit_legacy/jbrowse/data/tracks.conf Diaphorina_citri_legacy/ +cp /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/trackList.json Drosophila_biarmipes/ +cp /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/tracks.conf Drosophila_biarmipes/ +cp /app/data/modencode/drobip/Dbip_2.0/jbrowse/data/trackList.json Drosophila_bipectinata/ +cp /app/data/modencode/drobip/Dbip_2.0/jbrowse/data/tracks.conf Drosophila_bipectinata/ +cp /app/data/modencode/droele/Dele_2.0/jbrowse/data/trackList.json Drosophila_elegans/ +cp /app/data/modencode/droele/Dele_2.0/jbrowse/data/tracks.conf Drosophila_elegans/ +cp /app/data/modencode/droeug/Deug_2.0/jbrowse/data/trackList.json Drosophila_eugracilis/ +cp /app/data/modencode/droeug/Deug_2.0/jbrowse/data/tracks.conf Drosophila_eugracilis/ +cp /app/data/modencode/drofic/Dfic_2.0/jbrowse/data/trackList.json Drosophila_ficusphila/ +cp /app/data/modencode/drofic/Dfic_2.0/jbrowse/data/tracks.conf Drosophila_ficusphila/ +cp /app/data/modencode/drokik/Dkik_2.0/jbrowse/data/trackList.json Drosophila_kikkawai/ +cp /app/data/modencode/drokik/Dkik_2.0/jbrowse/data/tracks.conf Drosophila_kikkawai/ +cp /app/data/modencode/drorho/Drho_2.0/jbrowse/data/trackList.json Drosophila_rhopaloa/ +cp /app/data/modencode/drorho/Drho_2.0/jbrowse/data/tracks.conf Drosophila_rhopaloa/ +cp /app/data/modencode/drotak/Dtak_2.0/jbrowse/data/trackList.json Drosophila_takahashii/ +cp /app/data/modencode/drotak/Dtak_2.0/jbrowse/data/tracks.conf Drosophila_takahashii/ +cp /app/data/modencode/Drosophila_eugracilis/jbrowse/data/trackList.json Drosophila_eugracilis/ +cp /app/data/modencode/Drosophila_eugracilis/jbrowse/data/tracks.conf Drosophila_eugracilis/ +cp /app/data/other_species/dufnov/jbrowse/data/trackList.json Dufourea_novaeangliae/ +cp /app/data/other_species/dufnov/jbrowse/data/tracks.conf Dufourea_novaeangliae/ +cp /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/trackList.json Ephemera_danica/ +cp /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/tracks.conf Ephemera_danica/ +cp /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/trackList.json Eufriesea_mexicana/ +cp /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/tracks.conf Eufriesea_mexicana/ +cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json Eurytemora_affinis/ +cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/tracks.conf Eurytemora_affinis/ +cp /app/data/other_species/fopari/jbrowse/data/trackList.json Fopius_arisanus/ +cp /app/data/other_species/fopari/jbrowse/data/tracks.conf Fopius_arisanus/ +cp /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/trackList.json Frankliniella_occidentalis/ +cp /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/tracks.conf Frankliniella_occidentalis/ +cp /app/data/other_species/galmel/ASM364042v2/jbrowse/data/trackList.json Galleria_mellonella/ +cp /app/data/other_species/galmel/ASM364042v2/jbrowse/data/tracks.conf Galleria_mellonella/ +cp /app/data/BCM_i5k_pilot/gerbue/BCM/jbrowse/data//trackList.json Gerris_buenoi/ +cp /app/data/BCM_i5k_pilot/gerbue/BCM/jbrowse/data//tracks.conf Gerris_buenoi/ +cp /app/data/other_species/hablab/jbrowse/data/trackList.json Habropoda_laboriosa/ +cp /app/data/other_species/hablab/jbrowse/data/tracks.conf Habropoda_laboriosa/ +cp /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/trackList.json Halyomorpha_halys/ +cp /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/tracks.conf Halyomorpha_halys/ +cp /app/data/other_species/helvir/jbrowse/data//trackList.json Heliothis_virescens/ +cp /app/data/other_species/helvir/jbrowse/data//tracks.conf Heliothis_virescens/ +cp /app/data/other_species/holduo/ASM273828v1/jbrowse/data/trackList.json Holacanthella_duospinosa/ +cp /app/data/other_species/holduo/ASM273828v1/jbrowse/data/tracks.conf Holacanthella_duospinosa/ +cp /app/data/BCM_i5k_pilot/homvit/jbrowse/data/trackList.json Homalodisca_vitripennis/ +cp /app/data/BCM_i5k_pilot/homvit/jbrowse/data/tracks.conf Homalodisca_vitripennis/ +cp /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/trackList.json Hyalella_azteca/ +cp /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/tracks.conf Hyalella_azteca/ +cp /app/data/BCM_i5k_pilot/ladful/Lful_2.0/jbrowse/data/trackList.json Ladona_fulva/ +cp /app/data/BCM_i5k_pilot/ladful/Lful_2.0/jbrowse/data/tracks.conf Ladona_fulva/ +cp /app/data/other_species/laostr/ASM333518v2/jbrowse/data(remove3annotationstochange)/trackList.json Laodelphax_striatellus/ +cp /app/data/other_species/laostr/ASM333518v2/jbrowse/data(remove3annotationstochange)/tracks.conf Laodelphax_striatellus/ +cp /app/data/other_species/lasalb/jbrowse/data/trackList.json Lasioglossum_albipes/ +cp /app/data/other_species/lasalb/jbrowse/data/tracks.conf Lasioglossum_albipes/ +cp /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/trackList.json Latrodectus_hesperus/ +cp /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/tracks.conf Latrodectus_hesperus/ +cp /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/trackList.json Leptinotarsa_decemlineata/ +cp /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/tracks.conf Leptinotarsa_decemlineata/ +cp /app/data/BCM_i5k_pilot/limlun/Llun_2.0/jbrowse/data/trackList.json Limnephilus_lunatus/ +cp /app/data/BCM_i5k_pilot/limlun/Llun_2.0/jbrowse/data/tracks.conf Limnephilus_lunatus/ +cp /app/data/other_species/locmig/jbrowse/data//trackList.json Locusta_migratoria/ +cp /app/data/other_species/locmig/jbrowse/data//tracks.conf Locusta_migratoria/ +cp /app/data/BCM_i5k_pilot/loxrec/Lrec_1.0/jbrowse/data/trackList.json Loxosceles_reclusa/ +cp /app/data/BCM_i5k_pilot/loxrec/Lrec_1.0/jbrowse/data/tracks.conf Loxosceles_reclusa/ +cp /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/trackList.json Mamestra_configurata/ +cp /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/tracks.conf Mamestra_configurata/ +cp /app/data/other_species/mansex/jbrowse/data/trackList.json Manduca_sexta/ +cp /app/data/other_species/mansex/jbrowse/data/tracks.conf Manduca_sexta/ +cp /app/data/other_species/maydes/jbrowse/data/trackList.json Mayetiola_destructor/ +cp /app/data/other_species/maydes/jbrowse/data/tracks.conf Mayetiola_destructor/ +cp /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/trackList.json Medauroidea_extradentata/ +cp /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/tracks.conf Medauroidea_extradentata/ +cp /app/data/other_species/megrot/jbrowse/data/trackList.json Megachile_rotundata/ +cp /app/data/other_species/megrot/jbrowse/data/tracks.conf Megachile_rotundata/ +cp /app/data/other_species/melqua/jbrowse/data/trackList.json Melipona_quadrifasciata/ +cp /app/data/other_species/melqua/jbrowse/data/tracks.conf Melipona_quadrifasciata/ +cp /app/data/other_species/micdem/jbrowse/data/trackList.json Microplitis_demolitor/ +cp /app/data/other_species/micdem/jbrowse/data/tracks.conf Microplitis_demolitor/ +cp /app/data/other_species/apimel/Amel_HAv3.1/jbrowse/data/trackList.json Monica_testing/ +cp /app/data/other_species/apimel/Amel_HAv3.1/jbrowse/data/tracks.conf Monica_testing/ +cp /app/data/other_species/neolec/Nlec1.1/jbrowse/data//trackList.json Neodiprion_lecontei/ +cp /app/data/other_species/neolec/Nlec1.1/jbrowse/data//tracks.conf Neodiprion_lecontei/ +cp /app/data/other_species/neolec/jbrowse/data/trackList.json Neodiprion_lecontei_training/ +cp /app/data/other_species/neolec/jbrowse/data/tracks.conf Neodiprion_lecontei_training/ +cp /app/data/other_species/nicves/jbrowse/data/trackList.json Nicrophorus_vespilloides/ +cp /app/data/other_species/nicves/jbrowse/data/tracks.conf Nicrophorus_vespilloides/ +cp /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/trackList.json Nylanderia_fulva/ +cp /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/tracks.conf Nylanderia_fulva/ +cp /app/data/other_species/odobru/Obru_v1/jbrowse/data/trackList.json Odontomachus_brunneus/ +cp /app/data/other_species/odobru/Obru_v1/jbrowse/data/tracks.conf Odontomachus_brunneus/ +cp /app/data/BCM_i5k_pilot/oncfas/BCM/jbrowse/data/trackList.json Oncopeltus_fasciatus/ +cp /app/data/BCM_i5k_pilot/oncfas/BCM/jbrowse/data/tracks.conf Oncopeltus_fasciatus/ +cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json Oncopeltus_fasciatus_training/ +cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/tracks.conf Oncopeltus_fasciatus_training/ +cp /app/data/BCM_i5k_pilot/onttau/jbrowse/data/trackList.json Onthophagus_taurus/ +cp /app/data/BCM_i5k_pilot/onttau/jbrowse/data/tracks.conf Onthophagus_taurus/ +cp /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/trackList.json Orussus_abietinus/ +cp /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/tracks.conf Orussus_abietinus/ +cp /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/trackList.json Osmia_lignaria/ +cp /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/tracks.conf Osmia_lignaria/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_10/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_10/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_11/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_11/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_12/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_12/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_13/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_13/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_14/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_14/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_15/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_15/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_16/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_16/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_17/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_17/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_18/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_18/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_19/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_19/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_1/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_1/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_20/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_20/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_21/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_21/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_22/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_22/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_23/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_23/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_24/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_24/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_25/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_25/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_26/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_26/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_27/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_27/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_28/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_28/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_29/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_29/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_2/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_2/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_30/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_30/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_31/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_31/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_32/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_32/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_33/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_33/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_34/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_34/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_35/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_35/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_36/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_36/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_37/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_37/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_38/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_38/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_39/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_39/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_3/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_3/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_40/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_40/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_4/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_4/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_5/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_5/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_6/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_6/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_7/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_7/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_8/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_8/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json O._taurus_training_9/ +cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/tracks.conf O._taurus_training_9/ +cp /app/data/BCM_i5k_pilot/pacven/jbrowse/data/trackList.json Pachypsylla_venusta/ +cp /app/data/BCM_i5k_pilot/pacven/jbrowse/data/tracks.conf Pachypsylla_venusta/ +cp /app/data/BCM_i5k_pilot/partep/Ptep_2.0/jbrowse/data/trackList.json Parasteatoda_tepidariorum/ +cp /app/data/BCM_i5k_pilot/partep/Ptep_2.0/jbrowse/data/tracks.conf Parasteatoda_tepidariorum/ +cp /app/data/other_species/rhazep/jbrowse/data/trackList.json Rhagoletis_zephyria/ +cp /app/data/other_species/rhazep/jbrowse/data/tracks.conf Rhagoletis_zephyria/ +cp /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/trackList.json Rhyzopertha_dominica/ +cp /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/tracks.conf Rhyzopertha_dominica/ +cp /app/data/other_species/tesmon/Amel_HAv3.1/jbrowse/data/trackList.json Test_Monica/ +cp /app/data/other_species/tesmon/Amel_HAv3.1/jbrowse/data/tracks.conf Test_Monica/ +cp /app/data/other_species/tigcal/jbrowse/data/trackList.json Tigriopus_californicus/ +cp /app/data/other_species/tigcal/jbrowse/data/tracks.conf Tigriopus_californicus/ +cp /app/data/other_species/tricas/jbrowse/data/trackList.json Tribolium_castaneum/ +cp /app/data/other_species/tricas/jbrowse/data/tracks.conf Tribolium_castaneum/ +cp /app/data/BCM_i5k_pilot/tripre/jbrowse/data/trackList.json Trichogramma_pretiosum/ +cp /app/data/BCM_i5k_pilot/tripre/jbrowse/data/tracks.conf Trichogramma_pretiosum/ +cp /app/data/other_species/monpoe/Amel_4.5/jbrowse/data/trackList.json Tuesdays_test/ +cp /app/data/other_species/monpoe/Amel_4.5/jbrowse/data/tracks.conf Tuesdays_test/ +cp /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/trackList.json Varroa_destructor/ +cp /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/tracks.conf Varroa_destructor/ +cp /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/trackList.json Varroa_jacobsoni/ +cp /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/tracks.conf Varroa_jacobsoni/ diff --git a/organisms_orig/old/directory_listing.orifg b/organisms_orig/old/directory_listing.orifg new file mode 100644 index 0000000..c1aaac6 --- /dev/null +++ b/organisms_orig/old/directory_listing.orifg @@ -0,0 +1,85 @@ + Aethina | tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus | planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois | transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora | glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis | mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia | rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera | cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera | dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera | oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia | tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella | germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus | terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Bombus | impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Catajapyx | aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides | sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus | cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis | capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus | insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex | lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus | hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia | nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma | floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma | alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina | citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina | citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila | ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila | elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila | bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila | biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila | eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila | takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Drosophila | rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila | kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Dufourea | novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera | danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea | mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa | dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius | arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella | occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria | mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris | buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda | laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha | halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis | virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella | duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca | vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella | azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona | fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax | striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum | albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus | hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa | decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Leptinotarsa | decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Limnephilus | lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta | migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles | reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Manduca | sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola | destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea | extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile | rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona | quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis | demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion | lecontei_training | /app/data/other_species/neolec/jbrowse/data + Neodiprion | lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Nicrophorus | vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia | fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus | brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus | fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus | fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Onthophagus | taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + Orussus | abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia | lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla | venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda | tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis | zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus | microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha | dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Tigriopus | californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium | castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma | pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa | jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data + Varroa | destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Onthophagus | taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data diff --git a/organisms_orig/old/directory_listing.orig b/organisms_orig/old/directory_listing.orig new file mode 100644 index 0000000..c1aaac6 --- /dev/null +++ b/organisms_orig/old/directory_listing.orig @@ -0,0 +1,85 @@ + Aethina | tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus | planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois | transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora | glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis | mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia | rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera | cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera | dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera | oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia | tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella | germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus | terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Bombus | impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Catajapyx | aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides | sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus | cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis | capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus | insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex | lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus | hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia | nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma | floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma | alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina | citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina | citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila | ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila | elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila | bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila | biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila | eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila | takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Drosophila | rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila | kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Dufourea | novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera | danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea | mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa | dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius | arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella | occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria | mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris | buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda | laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha | halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis | virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella | duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca | vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella | azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona | fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax | striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum | albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus | hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa | decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Leptinotarsa | decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Limnephilus | lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta | migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles | reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Manduca | sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola | destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea | extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile | rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona | quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis | demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion | lecontei_training | /app/data/other_species/neolec/jbrowse/data + Neodiprion | lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Nicrophorus | vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia | fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus | brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus | fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus | fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Onthophagus | taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + Orussus | abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia | lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla | venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda | tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis | zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus | microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha | dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Tigriopus | californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium | castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma | pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa | jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data + Varroa | destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Onthophagus | taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data diff --git a/organisms_orig/old/directory_listing.txt b/organisms_orig/old/directory_listing.txt new file mode 100644 index 0000000..c1aaac6 --- /dev/null +++ b/organisms_orig/old/directory_listing.txt @@ -0,0 +1,85 @@ + Aethina | tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus | planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois | transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora | glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis | mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia | rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera | cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera | dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera | oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia | tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella | germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus | terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Bombus | impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Catajapyx | aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides | sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus | cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis | capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus | insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex | lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus | hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia | nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma | floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma | alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina | citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina | citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila | ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila | elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila | bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila | biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila | eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila | takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Drosophila | rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila | kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Dufourea | novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera | danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea | mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa | dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius | arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella | occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria | mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris | buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda | laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha | halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis | virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella | duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca | vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella | azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona | fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax | striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum | albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus | hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa | decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Leptinotarsa | decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Limnephilus | lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta | migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles | reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Manduca | sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola | destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea | extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile | rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona | quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis | demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion | lecontei_training | /app/data/other_species/neolec/jbrowse/data + Neodiprion | lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Nicrophorus | vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia | fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus | brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus | fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus | fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Onthophagus | taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + Orussus | abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia | lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla | venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda | tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis | zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus | microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha | dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Tigriopus | californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium | castaneum | 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Green - insertion in the read relative to the reference
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Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "File note" : "This track replaces the previous track, 'Aros_ID07'.", + "Alignment method" : "TopHat 2.0, default parameters", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Data Provider" : "Baylor College of Medicine" + }, + "label" : "Aros_ID07", + "type" : "WebApollo/View/Track/DraggableAlignments", + "category" : "Transcriptome/Mapped Reads", + "key" : "A. rosae male-2 raw reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/Aros_ID08.bam", + "metadata" : { + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C72E8FAE-2A8F-48CC-8E81-E763757DC126/align_summary.txt", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "File note" : "This track replaces the previous track, 'Aros_ID08'.", + "Alignment method" : "TopHat 2.0, default parameters", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Data Provider" : "Baylor College of Medicine" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "Aros_ID08", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae male-1 raw reads" + }, + { + "style" : { + "neg_color" : "rgba(255,255,0,50)", + "pos_color" : "rgba(0,0,255,50)" + }, + "bicolor_pivot" : "0.5", + "key" : "GC Content", + "scoreType": "avgScore", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Aros01112013-genome_GC.bigwig", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track contact" : "The i5k workspace@NAL" + }, + "type" : "JBrowse/View/Track/Wiggle/Density", + "label" : "GC Content" + }, + { + "style" : { + "neg_color" : "white", + "pos_color" : "black" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "key" : "Gaps in assembly", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Aros01112013-GAPS.bigwig", + "label" : "Gaps in assembly", + "metadata" : { + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", + "Track contact" : "The i5k workspace@NAL" + }, + "category" : "Reference Assembly", + "type" : "JBrowse/View/Track/Wiggle/Density" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "A. rosae females-combined Trinity transcriptome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/atro-females-comb_est2genome/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads from two females were concatenated and then assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Assembly", + "label" : "atro-females-comb_est2genome", + "type" : "FeatureTrack" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "A. rosae male-1 Trinity transcriptome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/atro-male-1_est2genome/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Assembly", + "label" : "atro-male-1_est2genome", + "type" : "FeatureTrack" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "A. rosae male-2 Trinity transcriptome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/atro-male-2_est2genome/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads were assembled using Trinity version trinityrnaseq_r20140413p1 using default settings. Assembled transcripts were mapped to the genome using Exonerate-gff3 (https://github.com/hotdogee/exonerate-gff3) with the options: --model est2genome --showtargetgff yes --gff3 yes --showalignment no --showvulgar no --geneseed 250 --bestn 2 --percent 50 --minintron 20 --maxintron 10000. Transcripts mapping to two locations were detected and marked with a note using a custom perl script (available from JP Oeyen (Univ. Bonn/ZFMK, ZMB), janphilipoyen@gmail.com)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Assembly", + "label" : "atro-male-2_est2genome", + "type" : "FeatureTrack" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_male-1_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae male-1 cleaned reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-2_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-63-1_2pA_D191TACXX-6-ID07_D191TACXX-6-ID07_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_male-2_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae male-2 cleaned reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_female-1_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae female-1 cleaned reads" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bam", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings.", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 " + }, + "category" : "Transcriptome/Mapped Reads", + "label" : "aros_female-2_tophat-accepted_hits", + "type" : "WebApollo/View/Track/DraggableAlignments", + "key" : "A. rosae female-2 cleaned reads" + }, + { + "style" : { + "clip_marker_color" : "red", + "pos_color" : "#FFA600", + "neg_color" : "#005EFF", + "height" : 50 + }, + "bicolor_pivot" : "zero", + "key" : " A. rosae female-1 cleaned reads, XY-plots", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-1_tophat-accepted_hits.bigwig", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.W-1544-1_2pA_D191TACXX-6-ID05_D191TACXX-6-ID05_2_sequence.txt.bz2" + }, + "category" : "Transcriptome/Coverage plots (BigWig)", + "label" : "aros_female-1_tophat-accepted_hits_bigwig" + }, + { + "style" : { + "clip_marker_color" : "red", + "pos_color" : "#FFA600", + "neg_color" : "#005EFF", + "height" : 50 + }, + "bicolor_pivot" : "zero", + "key" : " A. rosae female-2 cleaned reads, XY-plots", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_female-2_tophat-accepted_hits.bigwig", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. Alignment files were converted by the NAL to bigwig format; reads that failed QC, secondary and supplementary alignments, and optical or PCR duplicates were ignored.", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage.", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.WT-66-1_2pA_D191TACXX-6-ID06_D191TACXX-6-ID06_2_sequence.txt.bz2 " + }, + "category" : "Transcriptome/Coverage plots (BigWig)", + "label" : "aros_female-2_tophat-accepted_hits_bigwig" + }, + { + "style" : { + "clip_marker_color" : "red", + "pos_color" : "#FFA600", + "neg_color" : "#005EFF", + "height" : 50 + }, + "bicolor_pivot" : "zero", + "key" : " A. rosae male-1 cleaned reads, XY-plots", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/janphilipoeyen/Athalia_rosae/cleaned-reads-tophat/aros_male-1_tophat-accepted_hits.bigwig", + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "metadata" : { + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Turnip_sawfly/RNA_sequence/Aros_ICD_SFI5MH.sw-1228-WT-63-1_2pA_D191TACXX-6-ID08_D191TACXX-6-ID08_1_sequence.txt.bz2", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Method" : "Raw reads cleaned with Trimmomatic v0.32, using the options ILLUMINACLIP:'costumadapterlist.fa':2:30:10, SLIDINGWINDOW:4:33 and MINLEN:45. Cleaned reads mapped with TopHat v2.0.12 using default settings. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine" + } + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "protein2genome_Tardigrada", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "label" : "protein2genome_Tardigrada", + "type" : "FeatureTrack", + "category" : "BCM_v0.5.3/3. 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At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track contact" : "The i5k workspace@NAL" + } + }, + { + "style" : { + "pos_color" : "#00BFFF", + "neg_color" : "BG_RNAseq_heads_NCSU" + }, + "bicolor_pivot" : "zero", + "key" : "BG_RNAseq_heads_NCSU", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/TopHat2-SE_Lane1_2_Sample3_4_merged-2015-09-01-21-37-00.7/TopHat2-SE_Lane1_2_Sample3_4_merged.bam", + "metadata" : { + "RNA dataset name" : "BG_RNAseq_heads_NCSU", + "Species name" : "Blattella germanica", + "Data Source 3 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/BF73CC50-6318-4461-B672-6C83180CEA43/align_summary.txt", + "Note" : "This is merged dataset from four separate sources", + "Data Source 2 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/C417CB73-E609-49FB-89CC-EEA20455B734/align_summary.txt", + "Data Source 4 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/DAA3D4D7-4D22-451D-9914-EAD37D2E0A5B/align_summary.txt", + "Data Source 1 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/040B27B4-069D-4B29-9F17-851270ED0534/align_summary.txt", + "Data Provider" : "Coby Schal, NCSU" + }, + "type" : "WebApollo/View/Track/DraggableAlignments", + "category" : "Transcriptome/Mapped Reads", + "label" : "BG_RNAseq_heads_NCSU" + }, + { + "style" : { + "neg_color" : "BG_RNAseq_heads_NCSU", + "pos_color" : "#00BFFF" + }, + "bicolor_pivot" : "zero", + "key" : "BG_RNAseq_heads_NCSU (Coverage Plot)", + "autoscale" : "local", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/TopHat2-SE_Lane1_2_Sample3_4_merged-2015-09-01-21-37-00.7/TopHat2-SE_Lane1_2_Sample3_4_merged.bigwig", + "metadata" : { + "RNA dataset name" : "BG_RNAseq_heads_NCSU", + "Species name" : "Blattella germanica", + "Data Source 3 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/BF73CC50-6318-4461-B672-6C83180CEA43/align_summary.txt", + "Note" : "This is merged dataset from four separate sources", + "Data Source 2 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/C417CB73-E609-49FB-89CC-EEA20455B734/align_summary.txt", + "Data Source 4 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/DAA3D4D7-4D22-451D-9914-EAD37D2E0A5B/align_summary.txt", + "Data Source 1 Alignment Summary" : "http://de.iplantcollaborative.org/dl/d/040B27B4-069D-4B29-9F17-851270ED0534/align_summary.txt", + "Data Provider" : "Coby Schal, NCSU" + }, + "label" : "BG_RNAseq_heads_NCSU (Coverage Plot)", + "category" : "Transcriptome/Coverage Plots (BigWig)", + "type" : "JBrowse/View/Track/Wiggle/XYPlot" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/SRR1552487_SRR1552488_merged-2015-09-01-18-15-30.1/SRR1552487_SRR1552488_merged.bam", + "label" : "BG_RNAseq_heads_UW", + "type" : "WebApollo/View/Track/DraggableAlignments", + "category" : "Transcriptome/Mapped Reads", + "metadata" : { + "Data URL" : "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488", + "Alignment summary" : "PE_SRR1552487: http://de.iplantcollaborative.org/dl/d/C663364F-AAA3-427F-8DFD-27772ED2BDCB/align_summary.txt; PE_SRR1552488: http://de.iplantcollaborative.org/dl/d/908426A6-7915-4CB4-9EA7-ABDA19590C4F/align_summary.txt", + "Other notes" : "tophat parameters: PE_SRR1552487: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552487_read1.fastq' --file_query2 'SRR1552487_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'; PE_SRR1552488: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552488_read1.fastq' --file_query2 'SRR1552488_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'", + "Citation" : "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700", + "File provider" : "Kim Walden, UIUC", + "Data provider" : "Inez Anna Drinnenberg", + "Track legend" : "Reads from SRR1552487 and SRR1552488 were aligned to the B. germanica assembly in TopHat, and the resulting alignment files were merged. Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "key" : "BG_RNAseq_heads_UW" + }, + { + "style" : { + "pos_color" : "#00BFFF", + "neg_color" : "BG_RNAseq_heads_UW" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "key" : "BG_RNAseq_heads_UW (Coverage Plot)", + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "user_contributed_data/Blatella_transcriptome/SRR1552487_SRR1552488_merged-2015-09-01-18-15-30.1/SRR1552487_SRR1552488_merged-nosecondary.bigwig", + "metadata" : { + "Data URL" : "http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552487; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1552488", + "Other notes" : "tophat parameters: PE_SRR1552487: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552487_read1.fastq' --file_query2 'SRR1552487_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'; PE_SRR1552488: --align_reads 'serial' --mate-inner-dist '300' --file_query 'SRR1552488_read1.fastq' --file_query2 'SRR1552488_read2.fastq' --library-type 'fr-unstranded' --min-anchor-length '8' --splice-mismatches '0' --min-intron-length '70' --max-intron-length '50000' --min-isoform-fraction '0.15' --max-multihits '20' --min-segment-intron '50' --max-segment-intron '500000' --segment-mismatches '2' --segment-length '20' --num-threads '6' --user_database 'Bgermanica.scaffolds' --b2-sensitive --tophat_version '2.0.9' --bowtie_version '2.1.0'", + "Alignment summary" : "PE_SRR1552487: http://de.iplantcollaborative.org/dl/d/C663364F-AAA3-427F-8DFD-27772ED2BDCB/align_summary.txt; PE_SRR1552488: http://de.iplantcollaborative.org/dl/d/908426A6-7915-4CB4-9EA7-ABDA19590C4F/align_summary.txt", + "File provider" : "Kim Walden, UIUC", + "Citation" : "Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Elife. 2014 Sep 23;3. doi: 10.7554/eLife.03676.PMID:25247700", + "Data provider" : "Inez Anna Drinnenberg", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage. 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Lauderdale conditions of data re-use." + }, + "key" : "blastx_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Arthropoda" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Atelocerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cephalochordata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Chelicerata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cnidaria" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Craniata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "est" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. 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Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "container-10px", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/drotenberg/FO_454AllContigs_30793seqs.parse_updated.bam" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "FO_RNAseq_females", + "label" : "FO_RNAseq_females", + "metadata" : { + "Alignment method" : "TopHat", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/42FD83E1-1694-4394-A50A-53C7E049C905/align_summary.txt", + "Analysis provider" : "Dorith Rotenberg, Kansas State University", + "Data Source" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Western_flower_thrips/RNA_sequence/", + "Materials Source" : "Groups of whole bodies of females from a laboratory colony of Frankliniella occidentalis originating from the Kamilo Iki valley on the island of Oahu, Hawaii", + "Read cleaning method" : "Prior to tophatPE alignment, reads were trimmed and cleaned with Prinseq-lite", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark red or blue while the introns spanning the predicted splicing sites are light red or blue. Reads mapped to the forward strand are red; reads mapped to the reverse strand are blue. Indels and substitutions identified during the mapping are also color marked:
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Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Lauderdale conditions of data re-use." + }, + "key" : "blastx_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Atelocerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cephalochordata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Chelicerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cnidaria" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Craniata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "est" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Parazoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Placozoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Priapulida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tardigrada" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tunicata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_UNCATEGORISED" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "repeatmasker", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatmasker" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "repeatrunner", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatrunner" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "snap" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions", + "metadata" : { + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "snap_masked", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "snap_masked" + }, + { + "style" : { + "pos_color" : "black", + "neg_color" : "white" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank", + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", +}, + "key" : "Gaps in assembly", + + + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Gbue.scaffolds.50.fa.gaps.bigwig", + "label" : "Gaps in assembly", + "type" : "JBrowse/View/Track/Wiggle/Density" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "bam/darmisen/Gbue_ICD_GBi5AK.bam", + "metadata" : { + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)", + "Data source 1" : "http://de.iplantcollaborative.org/dl/d/0058E2C3-0661-4F81-9AF3-E0DC790885DD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_1_sequence.txt", + "Data source 2" : "http://de.iplantcollaborative.org/dl/d/F5E1D612-1F2F-48DA-88FF-9F321A4988AD/Gbue_ICD_GBi5AK.T7-mix-emb-ny-1M-1F-cross-2-1_1pA_D2FUUACXX-3-ID10_2_sequence.txt", + "File provider" : "David Armisen, Institut de genomique fonctionelle de Lyon", + "Publication status" : "Unpublished - please follow Toronto/Ft. 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Spanned regions (possible splice junctions): light blue
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Insertions in the read relative to the reference: green
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Spanned regions (possible splice junctions): light blue
Deletions in the read relative to the reference: red
Insertions in the read relative to the reference: green
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Deletions in the read relative to the reference: red
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Lauderdale conditions of data re-use." + }, + "key" : "blastx_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Craniata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. 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Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Lauderdale conditions of data re-use." + }, + "key" : "blastx_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Annelida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Arthropoda" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Atelocerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cephalochordata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Chelicerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Cnidaria" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Craniata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Crustacea" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Echinodermata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "est2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "key" : "est2genome", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "category" : "BCM_v0.5.3/3. Mapped DNA/Other", + "urlTemplate" : "tracks/est2genome/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est2genome" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "est" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Parazoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Placozoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Priapulida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tardigrada" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tunicata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_UNCATEGORISED" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "repeatmasker", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatmasker" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "repeatrunner", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatrunner" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "snap" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions", + "metadata" : { + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "snap_masked", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "snap_masked" + }, + { + "style" : { + "pos_color" : "black", + "neg_color" : "white" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. 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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/mdbv_all_sort.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Microplitis demolitor ovary DNA", + "key" : "Microplitis demolitor ovary DNA (Coverage Plot)", + "label" : "Microplitis demolitor ovary DNA (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739298/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420507", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1128/JVI.01388-15", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/3t4wo_sort.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Microplitis demolitor bracovirus DNA", + "key" : "Microplitis demolitor bracovirus DNA (Coverage Plot)", + "label" : "Microplitis demolitor bracovirus DNA (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739297/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420508", + "Method" : "bwa 0.7.15", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/mdbv_all_sort.bigwig" + }, + { + "category" : "Mapped DNA/Mapped Reads", + "key" : "Infected Chrysodeixis includens hemocytes", + "label" : "Infected Chrysodeixis includens hemocytes", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739316/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRX1047183/", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_hemo_sort_mdbv.bam" + }, + { + "category" : "Mapped DNA/Mapped Reads", + "key" : "Infected Chrysodeixis includens", + "label" : "Infected Chrysodeixis includens", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739318", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766325,SRX3766326,SRX3766328,SRX3766330,SRX3766333,SRX3766334", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_sort_mdbv.bam" + }, + { + "category" : "Mapped DNA/Mapped Reads", + "key" : "Infected Trichoplusia ni", + "label" : "Infected Trichoplusia ni", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739317/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766323,SRX3766324,SRX3766327,SRX3766329,SRX3766331,SRX3766332", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/t_sort_mdbv.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Coverage Plots (BigWig)", + "key" : "Infected Chrysodeixis includens hemocytes (Coverage Plot)", + "label" : "Infected Chrysodeixis includens hemocytes (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739316/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRX1047183/", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_hemo_sort_mdbv.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Coverage Plots (BigWig)", + "key" : "Infected Chrysodeixis includens (Coverage Plot)", + "label" : "Infected Chrysodeixis includens (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739318", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766325,SRX3766326,SRX3766328,SRX3766330,SRX3766333,SRX3766334", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/p_sort_mdbv.bigwig" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "Mapped DNA/Coverage Plots (BigWig)", + "key" : "Infected Trichoplusia ni (Coverage Plot)", + "label" : "Infected Trichoplusia ni (Coverage Plot)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739317", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "SRX3766323,SRX3766324,SRX3766327,SRX3766329,SRX3766331,SRX3766332", + "Method" : "hisat2 v2.1.0", + "Publication status" : "Published - please cite 10.1016/j.virol.2016.02.023", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "pos_color" : "#00BFFF" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "user_contributed_data/UGA_March_2018/t_sort_mdbv.bigwig" + }, + { + "category" : "Mapped DNA/Microplitis demolitor ovary DNA", + "key" : "Microplitis demolitor ovary DNA, mapped reads (1% coverage)", + "label" : "Microplitis demolitor ovary DNA, mapped reads (1% coverage)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739298/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420507", + "Method" : "bwa 0.7.15; Coverage reduced to 1% with GATK", + "Publication status" : "Published - please cite 10.1128/JVI.01388-15", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "user_contributed_data/UGA_March_2018/3t4wo_sort.RG.Reordered.RCfrac.bam" + }, + { + "category" : "Mapped DNA/Microplitis demolitor bracovirus DNA", + "key" : "Microplitis demolitor bracovirus DNA, mapped reads (0.1% coverage)", + "label" : "Microplitis demolitor bracovirus DNA, mapped reads (0.1% coverage)", + "metadata" : { + "Data description" : "https://i5k.nal.usda.gov/node/739297/", + "Data provider" : "Gaelen Burke, University of Georgia", + "Data source" : "https://www.ncbi.nlm.nih.gov/sra/SRR3420508", + "Method" : "bwa 0.7.15; Coverage reduced to 0.1% with GATK", + "Publication status" : "Published - please cite 10.1371/journal.pgen.1004660", + "Track legend" : "Mapped reads are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Lauderdale conditions of data re-use.", + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "snap" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "pooled RNA-seq - cleaned reads", + "label" : "pooled_RNA-seq_cleaned_reads", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. 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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
Light blue alignments: Spliced portion of read aligned to reverse strand
Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Dark blue alignments: Mapped portion of read aligned to reverse strand
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Nematomorpha", + "label" : "protein2genome_Nematomorpha", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Onychophora", + "label" : "protein2genome_Onychophora", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Parazoa", + "label" : "protein2genome_Parazoa", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Placozoa", + "label" : "protein2genome_Placozoa", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Platyhelminthes", + "label" : "protein2genome_Platyhelminthes", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Priapulida", + "label" : "protein2genome_Priapulida", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Tardigrada", + "label" : "protein2genome_Tardigrada", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_Tunicata", + "label" : "protein2genome_Tunicata", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "compress" : 0, + "key" : "protein2genome_UNCATEGORISED", + "label" : "protein2genome_UNCATEGORISED", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/2. 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Evidence/Repeats", + "compress" : 0, + "key" : "repeatrunner", + "label" : "repeatrunner", + "metadata" : { + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use.", + "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "repeat" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json" + }, + { + "category" : "BCM_v0.5.3/1. 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Lauderdale conditions of data re-use.", + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline." + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "webapollo-arrowhead", + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "snap" + } + }, + "trackType" : null, + "type" : "FeatureTrack", + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "pooled RNA-seq - cleaned reads", + "label" : "pooled_RNA-seq_cleaned_reads", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "bam/ivargas/cleaned_reads/accepted_hits.bam" + }, + { + "autoscale" : "local", + "bicolor_pivot" : "zero", + "category" : "RNA-Seq/Coverage Plots", + "key" : "pooled RNA-seq - cleaned reads, XY-plot", + "label" : "pooled RNA-seq - cleaned reads, XY-plot", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/C1F07955-A133-4B73-85B5-4D5E57AC764C/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "Quality and adapter trimming with Trimmomatic3.0 (parameters ILLUMINACLIP:Trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)", + "Track legend" : "This track represents an X-Y plot of RNA-Seq coverage. The y-axis represents the number of mapped reads. The scale of the y-axis changes with the maximum number of reads aligned in the browser region. The y-axis has a minimum value of abs(2000); areas with higher coverage are indicated by a red clip." + }, + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "style" : { + "clip_marker_color" : "red", + "height" : 50, + "neg_color" : "#005EFF", + "pos_color" : "#FFA600" + }, + "type" : "JBrowse/View/Track/Wiggle/XYPlot", + "urlTemplate" : "bam/ivargas/cleaned_reads/accepted_hits.bigwig" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "pooled RNA-seq - raw reads", + "label" : "pooled_RNA-seq_raw_reads", + "metadata" : { + "Alignment method" : "TopHat 2.0.9, option --b2-very-sensitive", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/653A7172-438A-4688-811C-FA92A8FD22E6/align_summary.txt", + "Data Provider" : "Baylor College of Medicine", + "Data Source 1" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_1_sequence.txt.bz2", + "Data Source 2" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-female-1-1_1pA_C1M7KACXX-7-ID03_2_sequence.txt.bz2", + "Data Source 3" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_1_sequence.txt.bz2", + "Data Source 4" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-adult-male-1-1_1pA_C22AGACXX-4-ID02_2_sequence.txt.bz2", + "Data Source 5" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_1_sequence.txt.bz2", + "Data Source 6" : "ftp://ftp.hgsc.bcm.edu/I5K-pilot/Milkweed_bug/RNA_sequence/Ofas_RNA_ICD_OFi5KP.RNA-juveniles-1-1_1pA_C22AGACXX-4-ID01_2_sequence.txt.bz2", + "Read cleaning method" : "None", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
Yellow - mismatch (hover over the mismatch to see what the snp is)" + }, + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "type" : "WebApollo/View/Track/DraggableAlignments", + "urlTemplate" : "bam/ivargas/raw_reads/accepted_hits.bam" + }, + { + "category" : "RNA-Seq/Mapped Reads", + "key" : "RNA-seq raw PE reads Andolfatto et al.", + "label" : "RNA-seq_Andolfatto_raw_PE_reads", + "metadata" : { + "Alignment method" : "--align_reads together --mate-inner-dist 50 --file_query Oncopeltus_fasciatus_PE_1.fq.gz --file_query2 Oncopeltus_fasciatus_PE_2.fq.gz --library-type fr-unstranded --min-anchor-length 8 --splice-mismatches 0 --min-intron-length 70 --max-intron-length 50000 --min-isoform-fraction 0.15 --max-multihits 20 --min-segment-intron 50 --max-segment-intron 500000 --segment-mismatches 2 --segment-length 20 --num-threads 6 --user_database Ofas.scaffolds.fa --b2-sensitive --tophat_version 2.0.9 --bowtie_version 2.1.0", + "Alignment summary" : "http://de.iplantcollaborative.org/dl/d/5671A470-68E8-4FF2-AA8F-B55A8CC74AFF/align_summary.txt", + "Data Source" : "http://genomics-pubs.princeton.edu/insect_genomics/data/Oncopeltus_fasciatus.tar", + "Read cleaning method" : "None", + "Track legend" : "These Tophat RNA-seq mapping results are displayed so that the parts corresponding to the actual reads are colored in dark blue while the introns spanning the predicted splicing sites are light blue. Indels and substitutions identified during the mapping are also color marked:
Red - deletion in the read relative to the reference
Green - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Red marking - deletion in the read relative to the reference
Green marking - insertion in the read relative to the reference
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Green marking - insertion in the read relative to the reference
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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Parazoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Placozoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "est-gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nemata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Nematomorpha" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Onychophora" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Parazoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Placozoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Priapulida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tardigrada" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Tunicata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "protein2genome_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_UNCATEGORISED" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from RepeatMasker as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "repeatmasker", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatmasker/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatmasker" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "repeat" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/2. Evidence/Repeats", + "metadata" : { + "Track legend" : "Results from Repeatrunner as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "repeatrunner", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/repeatrunner/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "repeatrunner" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "snap" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/1. Gene Sets/Supplementary Gene Predictions", + "metadata" : { + "Track legend" : "Results from the SNAP gene prediction software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Published - please cite https://doi.org/10.1186/s12915-017-0399-x if using this data in your research" + }, + "key" : "snap_masked", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/snap_masked/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "snap_masked" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "wholeCDS" : null, + "exon" : "container-100pct", + "CDS" : "transcriptome-cds", + "UTR" : "transcriptome-utr" + }, + "arrowheadClass" : "trellis-arrowhead" + }, + "key" : "Jpn_Pt_gene.model_oda", + "category" : "Transcriptome/Assembly", + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/Jpn_Pt_gene.model_oda/{refseq}/trackData.json", + "compress" : 0, + "metadata" : { + "Analysis method" : "Mapped the RNA-seq reads to Baylor's Pt-genome (Ptep01282013genome) with BLAT, and predicted genes and transcripts with cufflinks and cuffmerge using the RNA-seq mapping data together with EST and cDNA mapping data. We removed multiple-hit (>= 3) reads and one (scaffold with larger number) of two loci of two-hit reads", + "Data provider" : "Yasuko Akiyama-Oda and Hiroki Oda, JT Biohistory Research Hall", + "Source of materials" : "RNA-seq of embryonic libraries (stages 3, 5, 7, and 10)", + "Track information" : "Gene models predicted by Cufflinks/Cuffmerge based on mapping of RNA-seq reads" + }, + "type" : "FeatureTrack", + "label" : "Jpn_Pt_gene.model_oda" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BAM", + "urlTemplate" : "user_contributed_files/yaoda/EST_cDNA_Oda.bam", + "label" : "EST_oda", + "category" : "Transcriptome/Mapped ESTs", + "type" : "WebApollo/View/Track/DraggableAlignments", + "metadata" : { + "Accession number" : "The EST data are deposited in the DNA Data Bank of Japan under accession numbers FY216297–FY225483 and FY368221–FY381845.", + "Data provider" : "Yasuko Akiyama-Oda and Hiroki Oda, JT Biohistory Research Hall", + "Source of materials" : "The EST data are derived from the 5′ end of five P. tepidariorum embryo cDNA libraries at different stages: At_eW: mixed segmentation stages; eS6: early stage 6; eS7: early stage 7; S7: stage 7. The cDNA data are mostly from cDNAs cloned and sequenced in our laboratory but include several cDNAs retrieved from NCBI.", + "Track legend" : "This track is displayed so that aligned exons are colored in dark blue while the introns spanning the predicted splicing sites are light blue.", + "Track information" : "cDNA and EST data mapped with BLAT" + }, + "key" : "EST_oda" + }, + { + "style" : { + "pos_color" : "black", + "neg_color" : "white" + }, + "bicolor_pivot" : "zero", + "autoscale" : "local", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of gaps in the reference assembly. Basecalls of N are colored black. All other regions are left blank", + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", +}, + "key" : "Gaps in assembly", + + + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Ptep01282013.GAPS.bigwig", + "label" : "Gaps in assembly", + "type" : "JBrowse/View/Track/Wiggle/Density" + }, + { + "storeClass" : "JBrowse/Store/SeqFeature/BigWig", + "urlTemplate" : "bigwig/Ptep01282013.genome_GC.bigwig", + "style" : { + "neg_color" : "rgba(255,255,0,50)", + "pos_color" : "rgba(0,0,255,50)" + }, + "label" : "GC Content", + "type" : "JBrowse/View/Track/Wiggle/Density", + "scoreType": "avgScore", + "bicolor_pivot" : "0.5", + "category" : "Reference Assembly", + "metadata" : { + "Track legend" : "Visualization of GC/AT content in the reference assembly. Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track.", + "Track contact" : "The i5k workspace@NAL", + "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.", +}, + "key" : "GC Content", + "scoreType": "avgScore", + + + "autoscale" : "local" + } + ], + "names" : { + "url" : "names/", + "type" : "Hash" + }, + "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico", + "formatVersion" : 1, + "alwaysOnTracks" : "DNA,Annotations" +} diff --git a/working/dev/README b/working/dev/README new file mode 100644 index 0000000..4f1e72e --- /dev/null +++ b/working/dev/README @@ -0,0 +1,77 @@ +# added -----COMPLETE +# "scoreType" : "avgScore", to the onttau training instances + +# perl -pi -e "s/ \"storeClass\" \: \"JBrowse\/Store\/SeqFeature\/BigWig\"\,\n/ \"storeClass\" \: \"JBrowse\/Store\/SeqFeature\/BigWig\",\n \"scoreType\" : \"avgScore\",\n/g" 2*_-_Onthophagus_taurus_training/trackList.json less 20_-_Onthophagus_taurus_training/trackList.json + +# These are the files that need to have ColorByType tracks. These will need to be replaced with the new track type +# grep -c ColorByType ./*/*|grep -v ":0" +# ./Apis_mellifera/trackList.json:2 +# ./Bombus_impatiens/trackList.json:3 +# ./Bombus_terrestris/trackList.json:3 +# ./Cephus_cinctus/trackList.json:4 +# ./Chelonus_insularis/trackList.json:2 +# ./Contarinia_nasturtii/trackList.json:2 +# ./Diachasma_alloeum/trackList.json:2 +# ./Ephemera_danica/trackList.json:2 +# ./Eufriesea_mexicana/trackList.json:2 +# ./Frankliniella_occidentalis/trackList.json:2 +# ./Galleria_mellonella/trackList.json:2 +# ./Halyomorpha_halys/trackList.json:2 +# ./Hyalella_azteca/trackList.json:2 +# ./Laodelphax_striatellus/trackList.json:2 +# ./Manduca_sexta/trackList.json:2 +# ./Neodiprion_lecontei/trackList.json:4 +# ./Nylanderia_fulva/trackList.json:2 +# ./Odontomachus_brunneus/trackList.json:2 +# ./Osmia_lignaria/trackList.json:2 +# ./Varroa_destructor/trackList.json:2 +# ./Varroa_jacobsoni/trackList.json:2 + +# Also need to make sure the css has been update=d + + +# Also found that the cDNA_match tracks are showing up as transparent boxes. solution is to set "classname" : "{type}" +(base) ARSMDBE22209004:working chrislocal$ grep "cDNA_match" ./*/trackList.json +./Aethina_tumida/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_100_cDNA_match/{refseq}/trackData.json", +./Aethina_tumida/trackList.json: "label" : "NCBI_Annotation_Release_100_cDNA_match", +./Agrilus_planipennis/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_100_cDNA_match/{refseq}/trackData.json", +./Agrilus_planipennis/trackList.json: "label" : "NCBI_Annotation_Release_100_cDNA_match", +./Amyelois_transitella/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_100_cDNA_match/{refseq}/trackData.json", +./Amyelois_transitella/trackList.json: "label" : "NCBI_Annotation_Release_100_cDNA_match", +./Bactrocera_oleae/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_100_cDNA_match/{refseq}/trackData.json", +./Bactrocera_oleae/trackList.json: "label" : "NCBI_Annotation_Release_100_cDNA_match" +./Bactrocera_oleae/trackList.json: "cDNA_match" : "jamp_match" +./Bemisia_tabaci/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_100_cDNA_match/{refseq}/trackData.json", +./Bemisia_tabaci/trackList.json: "label" : "NCBI_Annotation_Release_100_cDNA_match" +./Drosophila_biarmipes/trackList.json: "label" : "NCBI_Annotation_Release_101_cDNA_match", +./Drosophila_biarmipes/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json" +./Drosophila_bipectinata/trackList.json: "label" : "NCBI_Annotation_Release_101_cDNA_match", +./Drosophila_bipectinata/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json" +./Drosophila_elegans/trackList.json: "label" : "NCBI_Annotation_Release_101_cDNA_match", +./Drosophila_elegans/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json" +./Drosophila_eugracilis/trackList.json: "label" : "NCBI_Annotation_Release_101_cDNA_match", +./Drosophila_eugracilis/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json" +./Drosophila_ficusphila/trackList.json: "label" : "NCBI_Annotation_Release_101_cDNA_match", +./Drosophila_ficusphila/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json" +./Drosophila_kikkawai/trackList.json: "label" : "NCBI_Annotation_Release_101_cDNA_match", +./Drosophila_kikkawai/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json" +./Drosophila_rhopaloa/trackList.json: "label" : "NCBI_Annotation_Release_101_cDNA_match", +./Drosophila_rhopaloa/trackList.json: "urlTemplate" : "tracks/NCBI_Annotation_Release_101_cDNA_match/{refseq}/trackData.json" +./Drosophila_takahashii/trackList.json: "label" 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Green - insertion in the read relative to the reference
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Green - insertion in the read relative to the reference
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Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Mollusca" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nemata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nemata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nemata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Nematomorpha proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Nematomorpha", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Nematomorpha/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Nematomorpha" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Onychophora proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Onychophora", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Onychophora/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Onychophora" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Parazoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Parazoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Parazoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Parazoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Placozoa proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Placozoa", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Placozoa/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Placozoa" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Platyhelminthes proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Platyhelminthes", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Platyhelminthes/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Platyhelminthes" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Priapulida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Priapulida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Priapulida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Priapulida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tardigrada proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tardigrada", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tardigrada/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tardigrada" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of Tunicata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_Tunicata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_Tunicata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_Tunicata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "blastx" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Supplementary: BlastX", + "metadata" : { + "Track legend" : "Results from Blastx alignments of a set of UNCATEGORISED proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "blastx_UNCATEGORISED", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/blastx_UNCATEGORISED/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "blastx_UNCATEGORISED" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "cegma" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Other", + "metadata" : { + "Track legend" : "Results from CEGMA alignments as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." +}, + "key" : "cegma", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/cegma/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "cegma" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "est_gff" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/4. Transcriptome/Assembly", + "metadata" : { + "Track legend" : "Results from EST alignments resulting from the Cufflinks software as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "est_gff:cufflinks_i5k", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/est_gff:cufflinks_i5k/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "est_gff:cufflinks_i5k" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Annelida proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Annelida", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Annelida/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Annelida" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Arthropoda proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Arthropoda", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Arthropoda/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Arthropoda" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Atelocerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Atelocerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Atelocerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Atelocerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cephalochordata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cephalochordata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cephalochordata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cephalochordata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Chelicerata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Chelicerata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Chelicerata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Chelicerata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Cnidaria proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Cnidaria", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Cnidaria/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Cnidaria" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Craniata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Craniata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Craniata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Craniata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Crustacea proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Crustacea", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Crustacea/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Crustacea" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Echinodermata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Echinodermata", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Echinodermata/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Echinodermata" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Mollusca proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. Additional post-processing of the gene predictions was performed.", + "Publication status" : "Unpublished - please follow Toronto/Ft. Lauderdale conditions of data re-use." + }, + "key" : "protein2genome_Mollusca", + + + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "trackType" : null, + "urlTemplate" : "tracks/protein2genome_Mollusca/{refseq}/trackData.json", + "compress" : 0, + "type" : "FeatureTrack", + "label" : "protein2genome_Mollusca" + }, + { + "style" : { + "className" : "{type}", + "subfeatureClasses" : { + "match_part" : "protein2genome" + }, + "arrowheadClass" : "webapollo-arrowhead" + }, + "category" : "BCM_v0.5.3/3. Mapped Proteins/Protein2genome", + "metadata" : { + "Track legend" : "Results from Protein2genome alignments of a set of Nemata proteins as part of the MAKER automated annotation pipeline.", + "Analysis contact" : "Daniel Hughes, Baylor College of Medicine", + "Analysis description" : "The MAKER automated annotation software was run using RNA-Seq, protein homology from a wide taxonomic range, and CEGMA proteins as external evidence. 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status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use", + "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Varroa_jacobsoni/README_CURRENT_RELEASE", + "Data provider" : "NCBI", + "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/532/875/GCF_002532875.1_vjacob_1.0/GCF_002532875.1_vjacob_1.0_genomic.gff.gz", + "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/" + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "trellis-arrowhead", + "className" : "{type}", + "description" : "product, note, description", + "subfeatureClasses" : { + "CDS" : "gnomon_CDS", + "UTR" : "gnomon_UTR", + "exon" : "container-100pct", + "wholeCDS" : null + } + }, + "trackType" : "HTMLFeatures", + "type" : "HTMLFeatures", + "urlTemplate" : "tracks/varjac_current_models/{refseq}/trackData.json" + }, + { + "category" : "NCBI Annotation Release 100", + "compress" : 0, + "key" : "NCBI_Annotation_Release_100_Pseudogene", + "label" : "NCBI_Annotation_Release_100_Pseudogene", + "metadata" : { + "Publication status" : "Unpublished, please refer to Fort Lauderdale/Toronto conditions of data re-use", + "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Varroa_jacobsoni/README_CURRENT_RELEASE", + "Data provider" : "NCBI", + "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/532/875/GCF_002532875.1_vjacob_1.0/GCF_002532875.1_vjacob_1.0_genomic.gff.gz", + "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/" + }, + "storeClass" : "JBrowse/Store/SeqFeature/NCList", + "style" : { + "arrowheadClass" : "trellis-arrowhead", + "className" : "{type}", + "description" : "product, note, description", + "subfeatureClasses" : { + "CDS" : "gnomon_CDS", + "UTR" : "gnomon_UTR", + "exon" : "container-100pct", + "wholeCDS" : null + } + }, + "trackType" : "HTMLFeatures", + "type" : "HTMLFeatures", + "urlTemplate" : "tracks/NCBI_Annotation_Release_100_Pseudogene/{refseq}/trackData.json" + } + ] +} diff --git a/working/dev/command_file.sh b/working/dev/command_file.sh new file mode 100644 index 0000000..ff9699d --- /dev/null +++ b/working/dev/command_file.sh @@ -0,0 +1,125 @@ +mkdir Aethina_tumida; cd Aethina_tumida; cp /app/data/other_species/aettum/jbrowse/data/trackList.json .; cd .. +mkdir Agrilus_planipennis; cd Agrilus_planipennis; cp /app/data/BCM_i5k_pilot/agrpla/jbrowse/data/trackList.json .; cd .. +mkdir Amyelois_transitella; cd Amyelois_transitella; cp /app/data/other_species/amytra/jbrowse/data/trackList.json .; cd .. +mkdir Anoplophora_glabripennis; cd Anoplophora_glabripennis; cp /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Apis_mellifera; cd Apis_mellifera; cp /app/data/other_species/apimel/Amel_4.5/jbrowse/data//trackList.json .; cd .. +mkdir Athalia_rosae; cd Athalia_rosae; cp /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Bactrocera_cucurbitae; cd Bactrocera_cucurbitae; cp /app/data/other_species/baccuc/jbrowse/data/trackList.json .; cd .. +mkdir Bactrocera_dorsalis; cd Bactrocera_dorsalis; cp /app/data/other_species/bacdor/jbrowse/data/trackList.json .; cd .. +mkdir Bactrocera_oleae; cd Bactrocera_oleae; cp /app/data/other_species/bacole/jbrowse/data/trackList.json .; cd .. +mkdir Bemisia_tabaci; cd Bemisia_tabaci; cp /app/data/other_species/bemtab/jbrowse/data/trackList.json .; cd .. +mkdir Blattella_germanica; cd Blattella_germanica; cp /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Bombus_terrestris; cd Bombus_terrestris; cp /app/data/other_species/bomter/Bter_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Bombus_impatiens; cd Bombus_impatiens; cp /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data/trackList.json .; cd .. +mkdir Catajapyx_aquilonaris; cd Catajapyx_aquilonaris; cp /app/data/BCM_i5k_pilot/cataqu/jbrowse/data/trackList.json .; cd .. +mkdir Centruroides_sculpturatus; cd Centruroides_sculpturatus; cp /app/data/BCM_i5k_pilot/censcu/jbrowse/data/trackList.json .; cd .. +mkdir Cephus_cinctus; cd Cephus_cinctus; cp /app/data/other_species/cepcin/Ccin1/jbrowse/data//trackList.json .; cd .. +mkdir Ceratitis_capitata; cd Ceratitis_capitata; cp /app/data/BCM_i5k_pilot/cercap/jbrowse/data/trackList.json .; cd .. +mkdir Chelonus_insularis; cd Chelonus_insularis; cp /app/data/other_species/cheins/ASM1335770v1/jbrowse/data/trackList.json .; cd .. +mkdir Cimex_lectularius; cd Cimex_lectularius; cp /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Clitarchus_hookeri; cd Clitarchus_hookeri; cp /app/data/other_species/clihoo/jbrowse/data/trackList.json .; cd .. +mkdir Contarinia_nasturtii; cd Contarinia_nasturtii; cp /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data/trackList.json .; cd .. +mkdir Copidosoma_floridanum; cd Copidosoma_floridanum; cp /app/data/BCM_i5k_pilot/copflo/jbrowse/data/trackList.json .; cd .. +mkdir Diachasma_alloeum; cd Diachasma_alloeum; cp /app/data/other_species/diaall/Dall2.0/jbrowse/data/trackList.json .; cd .. +mkdir Diaphorina_citri; cd Diaphorina_citri; cp /app/data/other_species/diacit/jbrowse/data/trackList.json .; cd .. +mkdir Diaphorina_citri_legacy; cd Diaphorina_citri_legacy; cp /app/data/other_species/diacit_legacy/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_ficusphila; cd Drosophila_ficusphila; cp /app/data/modencode/drofic/Dfic_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_elegans; cd Drosophila_elegans; cp /app/data/modencode/droele/Dele_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_bipectinata; cd Drosophila_bipectinata; cp /app/data/modencode/drobip/Dbip_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_biarmipes; cd Drosophila_biarmipes; cp /app/data/modencode/drobia/Dbia_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_eugracilis; cd Drosophila_eugracilis; cp /app/data/modencode/droeug/Deug_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_takahashii; cd Drosophila_takahashii; cp /app/data/modencode/drotak/Dtak_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_rhopaloa; cd Drosophila_rhopaloa; cp /app/data/modencode/drorho/Drho_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Drosophila_kikkawai; cd Drosophila_kikkawai; cp /app/data/modencode/drokik/Dkik_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Dufourea_novaeangliae; cd Dufourea_novaeangliae; cp /app/data/other_species/dufnov/jbrowse/data/trackList.json .; cd .. +mkdir Ephemera_danica; cd Ephemera_danica; cp /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data//trackList.json .; cd .. +mkdir Eufriesea_mexicana; cd Eufriesea_mexicana; cp /app/data/other_species/eufmex/ASM148370v1/jbrowse/data/trackList.json .; cd .. +mkdir Euglossa_dilemma; cd Euglossa_dilemma; cp /app/data/other_species/eugdil/jbrowse/data/trackList.json .; cd .. +mkdir Eurytemora_affinis_-_training; cd Eurytemora_affinis_-_training; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. +mkdir Eurytemora_affinis; cd Eurytemora_affinis; cp /app/data/BCM_i5k_pilot/euraff/jbrowse/data/trackList.json .; cd .. +mkdir Fopius_arisanus; cd Fopius_arisanus; cp /app/data/other_species/fopari/jbrowse/data/trackList.json .; cd .. +mkdir Frankliniella_occidentalis; cd Frankliniella_occidentalis; cp /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data/trackList.json .; cd .. +mkdir Galleria_mellonella; cd Galleria_mellonella; cp /app/data/other_species/galmel/ASM364042v2/jbrowse/data/trackList.json .; cd .. +mkdir Gerris_buenoi; cd Gerris_buenoi; cp /app/data/BCM_i5k_pilot/gerbue/jbrowse/data//trackList.json .; cd .. +mkdir Habropoda_laboriosa; cd Habropoda_laboriosa; cp /app/data/other_species/hablab/jbrowse/data/trackList.json .; cd .. +mkdir Halyomorpha_halys; cd Halyomorpha_halys; cp /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data/trackList.json .; cd .. +mkdir Heliothis_virescens; cd Heliothis_virescens; cp /app/data/other_species/helvir/jbrowse/data//trackList.json .; cd .. +mkdir Holacanthella_duospinosa; cd Holacanthella_duospinosa; cp /app/data/other_species/holduo/ASM273828v1/jbrowse/data/trackList.json .; cd .. +mkdir Homalodisca_vitripennis; cd Homalodisca_vitripennis; cp /app/data/BCM_i5k_pilot/homvit/jbrowse/data/trackList.json .; cd .. +mkdir Hyalella_azteca; cd Hyalella_azteca; cp /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data/trackList.json .; cd .. +mkdir Ladona_fulva; cd Ladona_fulva; cp /app/data/BCM_i5k_pilot/ladful/jbrowse/data/trackList.json .; cd .. +mkdir Laodelphax_striatellus; cd Laodelphax_striatellus; cp /app/data/other_species/laostr/ASM333518v2/jbrowse/data/trackList.json .; cd .. +mkdir Lasioglossum_albipes; cd Lasioglossum_albipes; cp /app/data/other_species/lasalb/jbrowse/data/trackList.json .; cd .. +mkdir Latrodectus_hesperus; cd Latrodectus_hesperus; cp /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data/trackList.json .; cd .. +mkdir Leptinotarsa_decemlineata_training; cd Leptinotarsa_decemlineata_training; cp /app/data/BCM_i5k_pilot/lepdec/jbrowse/data/trackList.json .; cd .. +mkdir Leptinotarsa_decemlineata; cd Leptinotarsa_decemlineata; cp /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data/trackList.json .; cd .. +mkdir Limnephilus_lunatus; cd Limnephilus_lunatus; cp /app/data/BCM_i5k_pilot/limlun/jbrowse/data/trackList.json .; cd .. +mkdir Locusta_migratoria; cd Locusta_migratoria; cp /app/data/other_species/locmig/jbrowse/data//trackList.json .; cd .. +mkdir Loxosceles_reclusa; cd Loxosceles_reclusa; cp /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data/trackList.json .; cd .. +mkdir Manduca_sexta; cd Manduca_sexta; cp /app/data/other_species/mansex/jbrowse/data/trackList.json .; cd .. +mkdir Mayetiola_destructor; cd Mayetiola_destructor; cp /app/data/other_species/maydes/jbrowse/data/trackList.json .; cd .. +mkdir Medauroidea_extradentata; cd Medauroidea_extradentata; cp /app/data/other_species/medext/GCA_003012365.1/jbrowse/data/trackList.json .; cd .. +mkdir Megachile_rotundata; cd Megachile_rotundata; cp /app/data/other_species/megrot/jbrowse/data/trackList.json .; cd .. +mkdir Melipona_quadrifasciata; cd Melipona_quadrifasciata; cp /app/data/other_species/melqua/jbrowse/data/trackList.json .; cd .. +mkdir Microplitis_demolitor; cd Microplitis_demolitor; cp /app/data/other_species/micdem/jbrowse/data/trackList.json .; cd .. +mkdir Neodiprion_lecontei_training; cd Neodiprion_lecontei_training; cp /app/data/other_species/neolec/jbrowse/data/trackList.json .; cd .. +mkdir Neodiprion_lecontei; cd Neodiprion_lecontei; cp /app/data/other_species/neolec/Nlec1.1/jbrowse/data/trackList.json .; cd .. +mkdir Nicrophorus_vespilloides; cd Nicrophorus_vespilloides; cp /app/data/other_species/nicves/jbrowse/data/trackList.json .; cd .. +mkdir Nylanderia_fulva; cd Nylanderia_fulva; cp /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Odontomachus_brunneus; cd Odontomachus_brunneus; cp /app/data/other_species/odobru/Obru_v1/jbrowse/data/trackList.json .; cd .. +mkdir Oncopeltus_fasciatus; cd Oncopeltus_fasciatus; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. +mkdir Oncopeltus_fasciatus_training; cd Oncopeltus_fasciatus_training; cp /app/data/BCM_i5k_pilot/oncfas/jbrowse/data/trackList.json .; cd .. +mkdir 33_-_Onthophagus_taurus_training; cd 33_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 2_-_Onthophagus_taurus_training; cd 2_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 10_-_Onthophagus_taurus_training; cd 10_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 39_-_Onthophagus_taurus_training; cd 39_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 31_-_Onthophagus_taurus_training; cd 31_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 35_-_Onthophagus_taurus_training; cd 35_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 40_-_Onthophagus_taurus_training; cd 40_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 36_-_Onthophagus_taurus_training; cd 36_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 37_-_Onthophagus_taurus_training; cd 37_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 18_-_Onthophagus_taurus_training; cd 18_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 19_-_Onthophagus_taurus_training; cd 19_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 20_-_Onthophagus_taurus_training; cd 20_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 22_-_Onthophagus_taurus_training; cd 22_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 25_-_Onthophagus_taurus_training; cd 25_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 38_-_Onthophagus_taurus_training; cd 38_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 7_-_Onthophagus_taurus_training; cd 7_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 3_-_Onthophagus_taurus_training; cd 3_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 4_-_Onthophagus_taurus_training; cd 4_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir Onthophagus_taurus; cd Onthophagus_taurus; cp /app/data/BCM_i5k_pilot/onttau/jbrowse/data/trackList.json .; cd .. +mkdir 8_-_Onthophagus_taurus_training; cd 8_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 5_-_Onthophagus_taurus_training; cd 5_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 6_-_Onthophagus_taurus_training; cd 6_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 9_-_Onthophagus_taurus_training; cd 9_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 13_-_Onthophagus_taurus_training; cd 13_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 12_-_Onthophagus_taurus_training; cd 12_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 15_-_Onthophagus_taurus_training; cd 15_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 14_-_Onthophagus_taurus_training; cd 14_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 16_-_Onthophagus_taurus_training; cd 16_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 17_-_Onthophagus_taurus_training; cd 17_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 1_-_Onthophagus_taurus_training; cd 1_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 11_-_Onthophagus_taurus_training; cd 11_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 32_-_Onthophagus_taurus_training; cd 32_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 21_-_Onthophagus_taurus_training; cd 21_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 23_-_Onthophagus_taurus_training; cd 23_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 24_-_Onthophagus_taurus_training; cd 24_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 26_-_Onthophagus_taurus_training; cd 26_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 27_-_Onthophagus_taurus_training; cd 27_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 28_-_Onthophagus_taurus_training; cd 28_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 34_-_Onthophagus_taurus_training; cd 34_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 29_-_Onthophagus_taurus_training; cd 29_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir 30_-_Onthophagus_taurus_training; cd 30_-_Onthophagus_taurus_training; cp /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data/trackList.json .; cd .. +mkdir Orussus_abietinus; cd Orussus_abietinus; cp /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data/trackList.json .; cd .. +mkdir Osmia_lignaria; cd Osmia_lignaria; cp /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Pachypsylla_venusta; cd Pachypsylla_venusta; cp /app/data/BCM_i5k_pilot/pacven/jbrowse/data/trackList.json .; cd .. +mkdir Parasteatoda_tepidariorum; cd Parasteatoda_tepidariorum; cp /app/data/BCM_i5k_pilot/partep/jbrowse/data/trackList.json .; cd .. +mkdir Rhagoletis_zephyria; cd Rhagoletis_zephyria; cp /app/data/other_species/rhazep/jbrowse/data/trackList.json .; cd .. +mkdir Rhipicephalus_microplus; cd Rhipicephalus_microplus; cp /app/data/other_species/rhimic/jbrowse/data/trackList.json .; cd .. +mkdir Rhyzopertha_dominica; cd Rhyzopertha_dominica; cp /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data/trackList.json .; cd .. +mkdir Tigriopus_californicus; cd Tigriopus_californicus; cp /app/data/other_species/tigcal/jbrowse/data/trackList.json .; cd .. +mkdir Tribolium_castaneum; cd Tribolium_castaneum; cp /app/data/other_species/tricas/jbrowse/data/trackList.json .; cd .. +mkdir Trichogramma_pretiosum; cd Trichogramma_pretiosum; cp /app/data/BCM_i5k_pilot/tripre/jbrowse/data/trackList.json .; cd .. +mkdir Varroa_jacobsoni; cd Varroa_jacobsoni; cp /app/data/other_species/varjac/vjacob_1.0/jbrowse/data/trackList.json .; cd .. +mkdir Varroa_destructor; cd Varroa_destructor; cp /app/data/other_species/vardes/Vdes_3.0/jbrowse/data/trackList.json .; cd .. +mkdir Mamestra_configurata; cd Mamestra_configurata; cp /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data/trackList.json .; cd .. diff --git a/working/dev/directory_list.orig b/working/dev/directory_list.orig new file mode 100644 index 0000000..cb20ddd --- /dev/null +++ b/working/dev/directory_list.orig @@ -0,0 +1,129 @@ +webapollo_2=# select common_name, directory from organism ORDER BY genus; + common_name | directory +------------------------------------+------------------------------------------------------------- + Aethina_tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus_planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois_transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora_glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis_mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia_rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera_cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera_dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera_oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia_tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella_germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus_terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Bombus_impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Catajapyx_aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides_sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus_cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis_capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus_insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex_lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus_hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia_nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma_floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma_alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina_citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina_citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila_ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila_elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila_bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila_biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila_eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila_takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Drosophila_rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila_kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Dufourea_novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera_danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea_mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa_dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora_affinis_-_training | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora_affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius_arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella_occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria_mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris_buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda_laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha_halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis_virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella_duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca_vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella_azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona_fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax_striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum_albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus_hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa_decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Leptinotarsa_decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Limnephilus_lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta_migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles_reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Manduca_sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola_destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea_extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile_rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona_quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis_demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion_lecontei_training | /app/data/other_species/neolec/jbrowse/data + Neodiprion_lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Nicrophorus_vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia_fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus_brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus_fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus_fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + 33_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 2_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 10_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 39_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 31_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 35_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 40_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 36_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 37_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 18_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 19_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 20_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 22_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 25_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 38_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 7_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 3_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 4_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + Onthophagus_taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + 8_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 5_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 6_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 9_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 13_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 12_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 15_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 14_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 16_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 17_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 1_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 11_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 32_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 21_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 23_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 24_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 26_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 27_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 28_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 34_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 29_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + 30_-_Onthophagus_taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data + Orussus_abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia_lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla_venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda_tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis_zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus_microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha_dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Tigriopus_californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium_castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma_pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa_jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data + Varroa_destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Mamestra_configurata | /app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data +(125 rows) diff --git a/working/dev/directory_list.txt b/working/dev/directory_list.txt new file mode 100644 index 0000000..710b05f --- /dev/null +++ b/working/dev/directory_list.txt @@ -0,0 +1,125 @@ +Aethina_tumida|/app/data/other_species/aettum/jbrowse/data +Agrilus_planipennis|/app/data/BCM_i5k_pilot/agrpla/jbrowse/data +Amyelois_transitella|/app/data/other_species/amytra/jbrowse/data +Anoplophora_glabripennis|/app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data +Apis_mellifera|/app/data/other_species/apimel/Amel_4.5/jbrowse/data/ +Athalia_rosae|/app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data +Bactrocera_cucurbitae|/app/data/other_species/baccuc/jbrowse/data +Bactrocera_dorsalis|/app/data/other_species/bacdor/jbrowse/data +Bactrocera_oleae|/app/data/other_species/bacole/jbrowse/data +Bemisia_tabaci|/app/data/other_species/bemtab/jbrowse/data +Blattella_germanica|/app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data +Bombus_terrestris|/app/data/other_species/bomter/Bter_1.0/jbrowse/data +Bombus_impatiens|/app/data/other_species/bomimp/BIMP_2.1/jbrowse/data +Catajapyx_aquilonaris|/app/data/BCM_i5k_pilot/cataqu/jbrowse/data +Centruroides_sculpturatus|/app/data/BCM_i5k_pilot/censcu/jbrowse/data +Cephus_cinctus|/app/data/other_species/cepcin/Ccin1/jbrowse/data/ +Ceratitis_capitata|/app/data/BCM_i5k_pilot/cercap/jbrowse/data +Chelonus_insularis|/app/data/other_species/cheins/ASM1335770v1/jbrowse/data +Cimex_lectularius|/app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data +Clitarchus_hookeri|/app/data/other_species/clihoo/jbrowse/data +Contarinia_nasturtii|/app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data +Copidosoma_floridanum|/app/data/BCM_i5k_pilot/copflo/jbrowse/data +Diachasma_alloeum|/app/data/other_species/diaall/Dall2.0/jbrowse/data +Diaphorina_citri|/app/data/other_species/diacit/jbrowse/data +Diaphorina_citri_legacy|/app/data/other_species/diacit_legacy/jbrowse/data +Drosophila_ficusphila|/app/data/modencode/drofic/Dfic_2.0/jbrowse/data +Drosophila_elegans|/app/data/modencode/droele/Dele_2.0/jbrowse/data +Drosophila_bipectinata|/app/data/modencode/drobip/Dbip_2.0/jbrowse/data +Drosophila_biarmipes|/app/data/modencode/drobia/Dbia_2.0/jbrowse/data +Drosophila_eugracilis|/app/data/modencode/droeug/Deug_2.0/jbrowse/data +Drosophila_takahashii|/app/data/modencode/drotak/Dtak_2.0/jbrowse/data +Drosophila_rhopaloa|/app/data/modencode/drorho/Drho_2.0/jbrowse/data +Drosophila_kikkawai|/app/data/modencode/drokik/Dkik_2.0/jbrowse/data +Dufourea_novaeangliae|/app/data/other_species/dufnov/jbrowse/data +Ephemera_danica|/app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ +Eufriesea_mexicana|/app/data/other_species/eufmex/ASM148370v1/jbrowse/data +Euglossa_dilemma|/app/data/other_species/eugdil/jbrowse/data +Eurytemora_affinis_-_training|/app/data/BCM_i5k_pilot/euraff/jbrowse/data +Eurytemora_affinis|/app/data/BCM_i5k_pilot/euraff/jbrowse/data +Fopius_arisanus|/app/data/other_species/fopari/jbrowse/data +Frankliniella_occidentalis|/app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data +Galleria_mellonella|/app/data/other_species/galmel/ASM364042v2/jbrowse/data +Gerris_buenoi|/app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ +Habropoda_laboriosa|/app/data/other_species/hablab/jbrowse/data +Halyomorpha_halys|/app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data +Heliothis_virescens|/app/data/other_species/helvir/jbrowse/data/ +Holacanthella_duospinosa|/app/data/other_species/holduo/ASM273828v1/jbrowse/data +Homalodisca_vitripennis|/app/data/BCM_i5k_pilot/homvit/jbrowse/data +Hyalella_azteca|/app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data +Ladona_fulva|/app/data/BCM_i5k_pilot/ladful/jbrowse/data +Laodelphax_striatellus|/app/data/other_species/laostr/ASM333518v2/jbrowse/data +Lasioglossum_albipes|/app/data/other_species/lasalb/jbrowse/data +Latrodectus_hesperus|/app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data +Leptinotarsa_decemlineata_training|/app/data/BCM_i5k_pilot/lepdec/jbrowse/data +Leptinotarsa_decemlineata|/app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data +Limnephilus_lunatus|/app/data/BCM_i5k_pilot/limlun/jbrowse/data +Locusta_migratoria|/app/data/other_species/locmig/jbrowse/data/ +Loxosceles_reclusa|/app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data +Manduca_sexta|/app/data/other_species/mansex/jbrowse/data +Mayetiola_destructor|/app/data/other_species/maydes/jbrowse/data +Medauroidea_extradentata|/app/data/other_species/medext/GCA_003012365.1/jbrowse/data +Megachile_rotundata|/app/data/other_species/megrot/jbrowse/data +Melipona_quadrifasciata|/app/data/other_species/melqua/jbrowse/data +Microplitis_demolitor|/app/data/other_species/micdem/jbrowse/data +Neodiprion_lecontei_training|/app/data/other_species/neolec/jbrowse/data +Neodiprion_lecontei|/app/data/other_species/neolec/Nlec1.1/jbrowse/data +Nicrophorus_vespilloides|/app/data/other_species/nicves/jbrowse/data +Nylanderia_fulva|/app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data +Odontomachus_brunneus|/app/data/other_species/odobru/Obru_v1/jbrowse/data +Oncopeltus_fasciatus|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data +Oncopeltus_fasciatus_training|/app/data/BCM_i5k_pilot/oncfas/jbrowse/data +33_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +2_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +10_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +39_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +31_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +35_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +40_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +36_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +37_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +18_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +19_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +20_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +22_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +25_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +38_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +7_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +3_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +4_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +Onthophagus_taurus|/app/data/BCM_i5k_pilot/onttau/jbrowse/data +8_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +5_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +6_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +9_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +13_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +12_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +15_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +14_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +16_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +17_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +1_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +11_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +32_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +21_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +23_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +24_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +26_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +27_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +28_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +34_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +29_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +30_-_Onthophagus_taurus_training|/app/data/BCM_i5k_pilot/onttau_training/jbrowse/data +Orussus_abietinus|/app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data +Osmia_lignaria|/app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data +Pachypsylla_venusta|/app/data/BCM_i5k_pilot/pacven/jbrowse/data +Parasteatoda_tepidariorum|/app/data/BCM_i5k_pilot/partep/jbrowse/data +Rhagoletis_zephyria|/app/data/other_species/rhazep/jbrowse/data +Rhipicephalus_microplus|/app/data/other_species/rhimic/jbrowse/data +Rhyzopertha_dominica|/app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data +Tigriopus_californicus|/app/data/other_species/tigcal/jbrowse/data +Tribolium_castaneum|/app/data/other_species/tricas/jbrowse/data +Trichogramma_pretiosum|/app/data/BCM_i5k_pilot/tripre/jbrowse/data +Varroa_jacobsoni|/app/data/other_species/varjac/vjacob_1.0/jbrowse/data +Varroa_destructor|/app/data/other_species/vardes/Vdes_3.0/jbrowse/data +Mamestra_configurata|/app/data/other_species/mamcon/GCA_002192655.1/jbrowse/data diff --git a/working/dev/make_dir_script.pl b/working/dev/make_dir_script.pl new file mode 100644 index 0000000..5b2aa5f --- /dev/null +++ b/working/dev/make_dir_script.pl @@ -0,0 +1,9 @@ +#!/usr/bin/perl -w + +use strict; + +while (<>){ + $_ =~ m/(\S*)\|(\S*)/; + print "mkdir $1; cd $1; cp $2/trackList.json .; cd .. \n"; +} + diff --git a/working/dev/old/directory_listing.orifg b/working/dev/old/directory_listing.orifg new file mode 100644 index 0000000..c1aaac6 --- /dev/null +++ b/working/dev/old/directory_listing.orifg @@ -0,0 +1,85 @@ + Aethina | tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus | planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois | transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora | glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis | mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia | rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera | cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera | dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera | oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia | tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella | germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus | terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Bombus | impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Catajapyx | aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides | sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus | cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis | capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus | insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex | lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus | hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia | nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma | floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma | alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina | citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina | citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila | ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila | elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila | bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila | biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila | eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila | takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Drosophila | rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila | kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Dufourea | novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera | danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea | mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa | dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius | arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella | occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria | mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris | buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda | laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha | halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis | virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella | duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca | vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella | azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona | fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax | striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum | albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus | hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa | decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Leptinotarsa | decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Limnephilus | lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta | migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles | reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Manduca | sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola | destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea | extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile | rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona | quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis | demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion | lecontei_training | /app/data/other_species/neolec/jbrowse/data + Neodiprion | lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Nicrophorus | vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia | fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus | brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus | fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus | fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Onthophagus | taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + Orussus | abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia | lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla | venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda | tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis | zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus | microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha | dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Tigriopus | californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium | castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma | pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa | jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data + Varroa | destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Onthophagus | taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data diff --git a/working/dev/old/directory_listing.orig b/working/dev/old/directory_listing.orig new file mode 100644 index 0000000..c1aaac6 --- /dev/null +++ b/working/dev/old/directory_listing.orig @@ -0,0 +1,85 @@ + Aethina | tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus | planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois | transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora | glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis | mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia | rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera | cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera | dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera | oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia | tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella | germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus | terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Bombus | impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Catajapyx | aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides | sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus | cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis | capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus | insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex | lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus | hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia | nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma | floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma | alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina | citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina | citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila | ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila | elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila | bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila | biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila | eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila | takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Drosophila | rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila | kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Dufourea | novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera | danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea | mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa | dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius | arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella | occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria | mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris | buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda | laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha | halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis | virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella | duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca | vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella | azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona | fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax | striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum | albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus | hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa | decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Leptinotarsa | decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Limnephilus | lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta | migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles | reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Manduca | sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola | destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea | extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile | rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona | quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis | demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion | lecontei_training | /app/data/other_species/neolec/jbrowse/data + Neodiprion | lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Nicrophorus | vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia | fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus | brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus | fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus | fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Onthophagus | taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + Orussus | abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia | lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla | venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda | tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis | zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus | microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha | dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Tigriopus | californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium | castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma | pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa | jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data + Varroa | destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Onthophagus | taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data diff --git a/working/dev/old/directory_listing.txt b/working/dev/old/directory_listing.txt new file mode 100644 index 0000000..c1aaac6 --- /dev/null +++ b/working/dev/old/directory_listing.txt @@ -0,0 +1,85 @@ + Aethina | tumida | /app/data/other_species/aettum/jbrowse/data + Agrilus | planipennis | /app/data/BCM_i5k_pilot/agrpla/jbrowse/data + Amyelois | transitella | /app/data/other_species/amytra/jbrowse/data + Anoplophora | glabripennis | /app/data/BCM_i5k_pilot/anogla/BCM/jbrowse/data + Apis | mellifera | /app/data/other_species/apimel/Amel_4.5/jbrowse/data/ + Athalia | rosae | /app/data/BCM_i5k_pilot/athros/BCM/jbrowse/data + Bactrocera | cucurbitae | /app/data/other_species/baccuc/jbrowse/data + Bactrocera | dorsalis | /app/data/other_species/bacdor/jbrowse/data + Bactrocera | oleae | /app/data/other_species/bacole/jbrowse/data + Bemisia | tabaci | /app/data/other_species/bemtab/jbrowse/data + Blattella | germanica | /app/data/BCM_i5k_pilot/blager/BCM/jbrowse/data + Bombus | terrestris | /app/data/other_species/bomter/Bter_1.0/jbrowse/data + Bombus | impatiens | /app/data/other_species/bomimp/BIMP_2.1/jbrowse/data + Catajapyx | aquilonaris | /app/data/BCM_i5k_pilot/cataqu/jbrowse/data + Centruroides | sculpturatus | /app/data/BCM_i5k_pilot/censcu/jbrowse/data + Cephus | cinctus | /app/data/other_species/cepcin/Ccin1/jbrowse/data/ + Ceratitis | capitata | /app/data/BCM_i5k_pilot/cercap/jbrowse/data + Chelonus | insularis | /app/data/other_species/cheins/ASM1335770v1/jbrowse/data + Cimex | lectularius | /app/data/BCM_i5k_pilot/cimlec/BCM/jbrowse/data + Clitarchus | hookeri | /app/data/other_species/clihoo/jbrowse/data + Contarinia | nasturtii | /app/data/other_species/connas/AAFC_CNas_1.1/jbrowse/data + Copidosoma | floridanum | /app/data/BCM_i5k_pilot/copflo/jbrowse/data + Diachasma | alloeum | /app/data/other_species/diaall/Dall2.0/jbrowse/data + Diaphorina | citri | /app/data/other_species/diacit/jbrowse/data + Diaphorina | citri_legacy | /app/data/other_species/diacit_legacy/jbrowse/data + Drosophila | ficusphila | /app/data/modencode/drofic/Dfic_2.0/jbrowse/data + Drosophila | elegans | /app/data/modencode/droele/Dele_2.0/jbrowse/data + Drosophila | bipectinata | /app/data/modencode/drobip/Dbip_2.0/jbrowse/data + Drosophila | biarmipes | /app/data/modencode/drobia/Dbia_2.0/jbrowse/data + Drosophila | eugracilis | /app/data/modencode/droeug/Deug_2.0/jbrowse/data + Drosophila | takahashii | /app/data/modencode/drotak/Dtak_2.0/jbrowse/data + Drosophila | rhopaloa | /app/data/modencode/drorho/Drho_2.0/jbrowse/data + Drosophila | kikkawai | /app/data/modencode/drokik/Dkik_2.0/jbrowse/data + Dufourea | novaeangliae | /app/data/other_species/dufnov/jbrowse/data + Ephemera | danica | /app/data/BCM_i5k_pilot/ephdan/Edan_2.0/jbrowse/data/ + Eufriesea | mexicana | /app/data/other_species/eufmex/ASM148370v1/jbrowse/data + Euglossa | dilemma | /app/data/other_species/eugdil/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Eurytemora | affinis | /app/data/BCM_i5k_pilot/euraff/jbrowse/data + Fopius | arisanus | /app/data/other_species/fopari/jbrowse/data + Frankliniella | occidentalis | /app/data/BCM_i5k_pilot/fraocc/Focc_3.0/jbrowse/data + Galleria | mellonella | /app/data/other_species/galmel/ASM364042v2/jbrowse/data + Gerris | buenoi | /app/data/BCM_i5k_pilot/gerbue/jbrowse/data/ + Habropoda | laboriosa | /app/data/other_species/hablab/jbrowse/data + Halyomorpha | halys | /app/data/BCM_i5k_pilot/halhal/Hhal_1.1/jbrowse/data + Heliothis | virescens | /app/data/other_species/helvir/jbrowse/data/ + Holacanthella | duospinosa | /app/data/other_species/holduo/ASM273828v1/jbrowse/data + Homalodisca | vitripennis | /app/data/BCM_i5k_pilot/homvit/jbrowse/data + Hyalella | azteca | /app/data/BCM_i5k_pilot/hyaazt/Hazt_2.0.1/jbrowse/data + Ladona | fulva | /app/data/BCM_i5k_pilot/ladful/jbrowse/data + Laodelphax | striatellus | /app/data/other_species/laostr/ASM333518v2/jbrowse/data + Lasioglossum | albipes | /app/data/other_species/lasalb/jbrowse/data + Latrodectus | hesperus | /app/data/BCM_i5k_pilot/lathes/GCA_000697925.1/jbrowse/data + Leptinotarsa | decemlineata_training | /app/data/BCM_i5k_pilot/lepdec/jbrowse/data + Leptinotarsa | decemlineata | /app/data/BCM_i5k_pilot/lepdec/Ldec_2.0/jbrowse/data + Limnephilus | lunatus | /app/data/BCM_i5k_pilot/limlun/jbrowse/data + Locusta | migratoria | /app/data/other_species/locmig/jbrowse/data/ + Loxosceles | reclusa | /app/data/BCM_i5k_pilot/loxrec/GCA_001188405.1/jbrowse/data + Manduca | sexta | /app/data/other_species/mansex/jbrowse/data + Mayetiola | destructor | /app/data/other_species/maydes/jbrowse/data + Medauroidea | extradentata | /app/data/other_species/medext/GCA_003012365.1/jbrowse/data + Megachile | rotundata | /app/data/other_species/megrot/jbrowse/data + Melipona | quadrifasciata | /app/data/other_species/melqua/jbrowse/data + Microplitis | demolitor | /app/data/other_species/micdem/jbrowse/data + Neodiprion | lecontei_training | /app/data/other_species/neolec/jbrowse/data + Neodiprion | lecontei | /app/data/other_species/neolec/Nlec1.1/jbrowse/data + Nicrophorus | vespilloides | /app/data/other_species/nicves/jbrowse/data + Nylanderia | fulva | /app/data/other_species/nylful/TAMU_Nfulva_1.0/jbrowse/data + Odontomachus | brunneus | /app/data/other_species/odobru/Obru_v1/jbrowse/data + Oncopeltus | fasciatus | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Oncopeltus | fasciatus_training | /app/data/BCM_i5k_pilot/oncfas/jbrowse/data + Onthophagus | taurus | /app/data/BCM_i5k_pilot/onttau/jbrowse/data + Orussus | abietinus | /app/data/BCM_i5k_pilot/oruabi/BCM/jbrowse/data + Osmia | lignaria | /app/data/other_species/osmlig/USDA_OLig_1.0/jbrowse/data + Pachypsylla | venusta | /app/data/BCM_i5k_pilot/pacven/jbrowse/data + Parasteatoda | tepidariorum | /app/data/BCM_i5k_pilot/partep/jbrowse/data + Rhagoletis | zephyria | /app/data/other_species/rhazep/jbrowse/data + Rhipicephalus | microplus | /app/data/other_species/rhimic/jbrowse/data + Rhyzopertha | dominica | /app/data/other_species/rhydom/RdoDt3_tmp/jbrowse/data + Tigriopus | californicus | /app/data/other_species/tigcal/jbrowse/data + Tribolium | castaneum | /app/data/other_species/tricas/jbrowse/data + Trichogramma | pretiosum | /app/data/BCM_i5k_pilot/tripre/jbrowse/data + Varroa | jacobsoni | /app/data/other_species/varjac/vjacob_1.0/jbrowse/data + Varroa | destructor | /app/data/other_species/vardes/Vdes_3.0/jbrowse/data + Onthophagus | taurus_training | /app/data/BCM_i5k_pilot/onttau_training/jbrowse/data