diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..58e3357 Binary files /dev/null and b/.DS_Store differ diff --git a/bin/quantify.sh b/bin/quantify.sh new file mode 100755 index 0000000..58788b2 --- /dev/null +++ b/bin/quantify.sh @@ -0,0 +1,10 @@ +#!/bin/bash +set -e +set -u + +annot=${1} +bam_file=${2} +pair_id=${3} + +cufflinks --no-update-check -q -G $annot ${bam_file} +mv transcripts.gtf transcript_${pair_id}.gtf diff --git a/data/.DS_Store b/data/.DS_Store new file mode 100644 index 0000000..0621fd9 Binary files /dev/null and b/data/.DS_Store differ diff --git a/data/ggal/.DS_Store b/data/ggal/.DS_Store new file mode 100644 index 0000000..d44215e Binary files /dev/null and b/data/ggal/.DS_Store differ diff --git a/my_transcripts/transcript_ggal_gut.gtf b/my_transcripts/transcript_ggal_gut.gtf new file mode 100644 index 0000000..2c0c84a --- /dev/null +++ b/my_transcripts/transcript_ggal_gut.gtf @@ -0,0 +1,57 @@ +1 Cufflinks transcript 9363 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9363 9365 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "1"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9492 9629 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "2"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9807 9899 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "3"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 17513 17627 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "4"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 25466 25515 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "5"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 26906 27051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "6"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28318 28489 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "7"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28902 28976 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "8"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 30102 30204 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "9"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 32102 32157 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "10"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 33998 34051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "11"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 34472 34535 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "12"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 39445 39533 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "13"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 44828 44911 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "14"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 46449 46518 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "15"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 48688 48794 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "16"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 52850 52983 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "17"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 54245 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "18"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks transcript 67033 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67033 67073 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "1"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67259 67616 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "2"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 71917 72009 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "3"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 77548 77649 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "4"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 89127 89264 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "5"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 90317 90429 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "6"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 91255 91753 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "7"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95137 95207 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "8"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95937 96066 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "9"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 97416 97534 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "10"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 98166 98279 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "11"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 99699 99842 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "12"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 105181 105231 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "13"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 106560 106602 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "14"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 107138 108673 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "15"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 112436 112682 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "16"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 113405 113494 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "17"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 114631 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "18"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks transcript 123889 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 123889 123999 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "1"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124324 124872 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "2"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124965 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "3"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks transcript 128066 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 128066 128393 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "1"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 136408 136502 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "2"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 145684 145782 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "3"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 146627 146737 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "4"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 147215 147358 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "5"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 148372 148548 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "6"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 150722 150813 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "7"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 151683 151712 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "8"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 152519 152713 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "9"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 158405 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "10"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks transcript 163981 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 163981 164109 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 165545 165776 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 167819 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; diff --git a/my_transcripts/transcript_ggal_liver.gtf b/my_transcripts/transcript_ggal_liver.gtf new file mode 100644 index 0000000..4a66b85 --- /dev/null +++ b/my_transcripts/transcript_ggal_liver.gtf @@ -0,0 +1,57 @@ +1 Cufflinks transcript 67033 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67033 67073 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "1"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67259 67616 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "2"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 71917 72009 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "3"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 77548 77649 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "4"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 89127 89264 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "5"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 90317 90429 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "6"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 91255 91753 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "7"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95137 95207 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "8"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95937 96066 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "9"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 97416 97534 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "10"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 98166 98279 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "11"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 99699 99842 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "12"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 105181 105231 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "13"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 106560 106602 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "14"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 107138 108673 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "15"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 112436 112682 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "16"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 113405 113494 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "17"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 114631 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "18"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks transcript 9363 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9363 9365 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "1"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9492 9629 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "2"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9807 9899 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "3"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 17513 17627 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "4"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 25466 25515 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "5"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 26906 27051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "6"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28318 28489 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "7"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28902 28976 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "8"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 30102 30204 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "9"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 32102 32157 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "10"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 33998 34051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "11"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 34472 34535 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "12"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 39445 39533 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "13"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 44828 44911 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "14"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 46449 46518 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "15"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 48688 48794 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "16"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 52850 52983 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "17"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 54245 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "18"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks transcript 123889 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 123889 123999 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "1"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124324 124872 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "2"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124965 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "3"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks transcript 163981 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 163981 164109 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 165545 165776 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 167819 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks transcript 128066 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 128066 128393 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "1"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 136408 136502 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "2"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 145684 145782 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "3"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 146627 146737 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "4"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 147215 147358 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "5"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 148372 148548 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "6"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 150722 150813 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "7"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 151683 151712 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "8"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 152519 152713 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "9"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 158405 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "10"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; diff --git a/my_transcripts/transcript_ggal_lung.gtf b/my_transcripts/transcript_ggal_lung.gtf new file mode 100644 index 0000000..4321b6a --- /dev/null +++ b/my_transcripts/transcript_ggal_lung.gtf @@ -0,0 +1,57 @@ +1 Cufflinks transcript 9363 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9363 9365 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "1"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9492 9629 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "2"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9807 9899 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "3"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 17513 17627 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "4"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 25466 25515 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "5"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 26906 27051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "6"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28318 28489 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "7"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28902 28976 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "8"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 30102 30204 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "9"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 32102 32157 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "10"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 33998 34051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "11"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 34472 34535 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "12"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 39445 39533 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "13"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 44828 44911 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "14"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 46449 46518 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "15"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 48688 48794 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "16"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 52850 52983 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "17"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 54245 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "18"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks transcript 67033 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67033 67073 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "1"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67259 67616 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "2"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 71917 72009 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "3"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 77548 77649 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "4"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 89127 89264 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "5"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 90317 90429 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "6"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 91255 91753 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "7"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95137 95207 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "8"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95937 96066 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "9"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 97416 97534 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "10"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 98166 98279 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "11"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 99699 99842 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "12"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 105181 105231 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "13"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 106560 106602 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "14"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 107138 108673 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "15"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 112436 112682 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "16"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 113405 113494 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "17"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 114631 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "18"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks transcript 123889 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 123889 123999 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "1"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124324 124872 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "2"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124965 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "3"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks transcript 163981 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 163981 164109 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 165545 165776 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 167819 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks transcript 128066 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 128066 128393 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "1"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 136408 136502 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "2"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 145684 145782 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "3"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 146627 146737 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "4"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 147215 147358 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "5"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 148372 148548 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "6"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 150722 150813 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "7"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 151683 151712 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "8"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 152519 152713 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "9"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 158405 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "10"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; diff --git a/nextflow.config b/nextflow.config index 89c0ca4..7fdaa7e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1 +1,7 @@ +docker.enabled = true process.container = 'nextflow/rnatoy:1.3' +process.cpus = 2 + +workflow.onComplete = { + println ( workflow.success ? "Done!" : "Oops .. something went wrong" ) +} diff --git a/results/transcript_ggal_gut.gtf b/results/transcript_ggal_gut.gtf new file mode 100644 index 0000000..2c0c84a --- /dev/null +++ b/results/transcript_ggal_gut.gtf @@ -0,0 +1,57 @@ +1 Cufflinks transcript 9363 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9363 9365 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "1"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9492 9629 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "2"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9807 9899 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "3"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 17513 17627 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "4"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 25466 25515 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "5"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 26906 27051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "6"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28318 28489 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "7"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28902 28976 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "8"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 30102 30204 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "9"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 32102 32157 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "10"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 33998 34051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "11"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 34472 34535 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "12"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 39445 39533 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "13"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 44828 44911 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "14"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 46449 46518 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "15"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 48688 48794 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "16"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 52850 52983 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "17"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 54245 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "18"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks transcript 67033 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67033 67073 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "1"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67259 67616 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "2"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 71917 72009 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "3"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 77548 77649 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "4"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 89127 89264 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "5"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 90317 90429 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "6"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 91255 91753 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "7"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95137 95207 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "8"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95937 96066 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "9"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 97416 97534 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "10"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 98166 98279 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "11"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 99699 99842 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "12"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 105181 105231 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "13"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 106560 106602 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "14"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 107138 108673 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "15"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 112436 112682 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "16"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 113405 113494 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "17"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 114631 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "18"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks transcript 123889 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 123889 123999 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "1"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124324 124872 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "2"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124965 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "3"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks transcript 128066 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 128066 128393 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "1"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 136408 136502 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "2"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 145684 145782 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "3"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 146627 146737 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "4"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 147215 147358 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "5"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 148372 148548 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "6"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 150722 150813 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "7"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 151683 151712 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "8"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 152519 152713 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "9"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 158405 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "10"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks transcript 163981 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 163981 164109 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 165545 165776 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 167819 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; diff --git a/results/transcript_ggal_liver.gtf b/results/transcript_ggal_liver.gtf new file mode 100644 index 0000000..2c0c84a --- /dev/null +++ b/results/transcript_ggal_liver.gtf @@ -0,0 +1,57 @@ +1 Cufflinks transcript 9363 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9363 9365 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "1"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9492 9629 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "2"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9807 9899 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "3"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 17513 17627 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "4"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 25466 25515 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "5"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 26906 27051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "6"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28318 28489 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "7"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28902 28976 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "8"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 30102 30204 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "9"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 32102 32157 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "10"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 33998 34051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "11"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 34472 34535 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "12"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 39445 39533 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "13"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 44828 44911 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "14"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 46449 46518 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "15"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 48688 48794 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "16"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 52850 52983 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "17"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 54245 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "18"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks transcript 67033 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67033 67073 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "1"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67259 67616 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "2"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 71917 72009 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "3"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 77548 77649 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "4"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 89127 89264 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "5"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 90317 90429 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "6"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 91255 91753 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "7"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95137 95207 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "8"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95937 96066 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "9"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 97416 97534 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "10"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 98166 98279 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "11"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 99699 99842 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "12"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 105181 105231 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "13"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 106560 106602 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "14"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 107138 108673 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "15"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 112436 112682 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "16"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 113405 113494 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "17"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 114631 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "18"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks transcript 123889 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 123889 123999 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "1"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124324 124872 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "2"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124965 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "3"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks transcript 128066 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 128066 128393 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "1"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 136408 136502 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "2"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 145684 145782 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "3"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 146627 146737 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "4"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 147215 147358 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "5"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 148372 148548 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "6"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 150722 150813 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "7"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 151683 151712 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "8"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 152519 152713 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "9"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 158405 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "10"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks transcript 163981 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 163981 164109 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 165545 165776 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 167819 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; diff --git a/results/transcript_ggal_lung.gtf b/results/transcript_ggal_lung.gtf new file mode 100644 index 0000000..2c0c84a --- /dev/null +++ b/results/transcript_ggal_lung.gtf @@ -0,0 +1,57 @@ +1 Cufflinks transcript 9363 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9363 9365 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "1"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9492 9629 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "2"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 9807 9899 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "3"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 17513 17627 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "4"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 25466 25515 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "5"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 26906 27051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "6"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28318 28489 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "7"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 28902 28976 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "8"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 30102 30204 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "9"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 32102 32157 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "10"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 33998 34051 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "11"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 34472 34535 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "12"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 39445 39533 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "13"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 44828 44911 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "14"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 46449 46518 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "15"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 48688 48794 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "16"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 52850 52983 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "17"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks exon 54245 54379 1000 + . gene_id "ENSGALG00000011847"; transcript_id "ENSGALT00000019330"; exon_number "18"; FPKM "2113.8663734268"; frac "1.000000"; conf_lo "387.901707"; conf_hi "3839.831040"; cov "0.848760"; +1 Cufflinks transcript 67033 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67033 67073 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "1"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 67259 67616 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "2"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 71917 72009 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "3"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 77548 77649 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "4"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 89127 89264 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "5"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 90317 90429 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "6"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 91255 91753 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "7"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95137 95207 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "8"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 95937 96066 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "9"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 97416 97534 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "10"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 98166 98279 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "11"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 99699 99842 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "12"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 105181 105231 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "13"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 106560 106602 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "14"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 107138 108673 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "15"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 112436 112682 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "16"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 113405 113494 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "17"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks exon 114631 114680 1000 + . gene_id "ENSGALG00000011854"; transcript_id "ENSGALT00000019339"; exon_number "18"; FPKM "21141.6111675039"; frac "1.000000"; conf_lo "17700.651334"; conf_hi "24582.571001"; cov "8.097849"; +1 Cufflinks transcript 123889 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 123889 123999 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "1"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124324 124872 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "2"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks exon 124965 125213 1000 + . gene_id "ENSGALG00000011856"; transcript_id "ENSGALT00000019343"; exon_number "3"; FPKM "10378.4209696951"; frac "1.000000"; conf_lo "4830.921615"; conf_hi "15925.920325"; cov "3.869490"; +1 Cufflinks transcript 128066 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 128066 128393 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "1"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 136408 136502 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "2"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 145684 145782 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "3"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 146627 146737 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "4"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 147215 147358 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "5"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 148372 148548 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "6"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 150722 150813 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "7"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 151683 151712 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "8"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 152519 152713 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "9"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks exon 158405 159323 1000 + . gene_id "ENSGALG00000011857"; transcript_id "ENSGALT00000019344"; exon_number "10"; FPKM "86619.4123692770"; frac "1.000000"; conf_lo "76962.938696"; conf_hi "96275.886043"; cov "32.724279"; +1 Cufflinks transcript 163981 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 163981 164109 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 165545 165776 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; +1 Cufflinks exon 167819 167913 1 - . gene_id "ENSGALG00000011859"; transcript_id "ENSGALT00000019347"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; diff --git a/rna-ex1.nf b/rna-ex1.nf index 32fe130..af6dd39 100644 --- a/rna-ex1.nf +++ b/rna-ex1.nf @@ -6,12 +6,11 @@ params.reads = "$baseDir/data/ggal/reads/ggal_gut_{1,2}.fq" params.annot = "$baseDir/data/ggal/annotation.gff" params.genome = "$baseDir/data/ggal/genome.fa" -/* - * prints user convenience +/* + * prints user convenience */ println "R N A T O Y P I P E L I N E " println "=================================" println "genome : ${params.genome}" println "annotat : ${params.annot}" println "reads : ${params.reads}" - diff --git a/rna-ex2.nf b/rna-ex2.nf index 2d0c798..f3c2d08 100644 --- a/rna-ex2.nf +++ b/rna-ex2.nf @@ -6,8 +6,8 @@ params.reads = "$baseDir/data/ggal/reads/ggal_gut_{1,2}.fq" params.annot = "$baseDir/data/ggal/annotation.gff" params.genome = "$baseDir/data/ggal/genome.fa" -/* - * prints user convenience +/* + * prints user convenience */ println "R N A T O Y P I P E L I N E " println "=================================" @@ -21,19 +21,19 @@ println "reads : ${params.reads}" */ genome_file = file(params.genome) annotation_file = file(params.annot) - + /* * Step 1. Builds the genome index required by the mapping process */ process buildIndex { - + input: file genome from genome_file - + output: file 'genome.index*' into genome_index - + """ bowtie2-build --threads ${task.cpus} ${genome} genome.index """ -} \ No newline at end of file +} diff --git a/rna-ex3.nf b/rna-ex3.nf index 6875495..3fa805c 100644 --- a/rna-ex3.nf +++ b/rna-ex3.nf @@ -6,8 +6,8 @@ params.reads = "$baseDir/data/ggal/reads/ggal_gut_{1,2}.fq" params.annot = "$baseDir/data/ggal/annotation.gff" params.genome = "$baseDir/data/ggal/genome.fa" -/* - * prints user convenience +/* + * prints user convenience */ println "R N A T O Y P I P E L I N E " println "=================================" @@ -21,18 +21,18 @@ println "reads : ${params.reads}" */ genome_file = file(params.genome) annotation_file = file(params.annot) - + /* * Step 1. Builds the genome index required by the mapping process */ process buildIndex { - + input: file genome from genome_file - + output: file 'genome.index*' into genome_index - + """ bowtie2-build --threads ${task.cpus} ${genome} genome.index """ @@ -40,7 +40,7 @@ process buildIndex { /* * Create the `read_pairs` channel that emits tuples containing three elements: - * the pair ID, the first read-pair file and the second read-pair file + * the pair ID, the first read-pair file and the second read-pair file */ read_pairs = Channel.fromFilePairs(params.reads, flat: true) - +read_pairs.println() diff --git a/rna-ex4.nf b/rna-ex4.nf index 4692fb7..c929543 100644 --- a/rna-ex4.nf +++ b/rna-ex4.nf @@ -6,8 +6,8 @@ params.reads = "$baseDir/data/ggal/reads/ggal_gut_{1,2}.fq" params.annot = "$baseDir/data/ggal/annotation.gff" params.genome = "$baseDir/data/ggal/genome.fa" -/* - * prints user convenience +/* + * prints user convenience */ println "R N A T O Y P I P E L I N E " println "=================================" @@ -21,18 +21,18 @@ println "reads : ${params.reads}" */ genome_file = file(params.genome) annotation_file = file(params.annot) - + /* * Step 1. Builds the genome index required by the mapping process */ process buildIndex { - + input: file genome from genome_file - + output: file 'genome.index*' into genome_index - + """ bowtie2-build --threads ${task.cpus} ${genome} genome.index """ @@ -40,7 +40,7 @@ process buildIndex { /* * Create the `read_pairs` channel that emits tuples containing three elements: - * the pair ID, the first read-pair file and the second read-pair file + * the pair ID, the first read-pair file and the second read-pair file */ read_pairs = Channel.fromFilePairs(params.reads, flat: true) @@ -48,18 +48,16 @@ read_pairs = Channel.fromFilePairs(params.reads, flat: true) * Step 2. Maps each read-pair by using Tophat2 mapper tool */ process mapping { - + input: - file 'genome.index.fa' from genome_file + file 'genome.index.fa' from genome_file file genome_index from genome_index set pair_id, file(read1), file(read2) from read_pairs - + output: set pair_id, "tophat_out/accepted_hits.bam" into bam - + """ tophat2 -p ${task.cpus} genome.index ${read1} ${read2} """ } - - diff --git a/rna-ex5.nf b/rna-ex5.nf index c8e4c22..870aa57 100644 --- a/rna-ex5.nf +++ b/rna-ex5.nf @@ -6,8 +6,8 @@ params.reads = "$baseDir/data/ggal/reads/ggal_gut_{1,2}.fq" params.annot = "$baseDir/data/ggal/annotation.gff" params.genome = "$baseDir/data/ggal/genome.fa" -/* - * prints user convenience +/* + * prints user convenience */ println "R N A T O Y P I P E L I N E " println "=================================" @@ -21,18 +21,18 @@ println "reads : ${params.reads}" */ genome_file = file(params.genome) annotation_file = file(params.annot) - + /* * Step 1. Builds the genome index required by the mapping process */ process buildIndex { - + input: file genome from genome_file - + output: file 'genome.index*' into genome_index - + """ bowtie2-build --threads ${task.cpus} ${genome} genome.index """ @@ -40,7 +40,7 @@ process buildIndex { /* * Create the `read_pairs` channel that emits tuples containing three elements: - * the pair ID, the first read-pair file and the second read-pair file + * the pair ID, the first read-pair file and the second read-pair file */ read_pairs = Channel.fromFilePairs(params.reads, flat: true) @@ -48,15 +48,15 @@ read_pairs = Channel.fromFilePairs(params.reads, flat: true) * Step 2. Maps each read-pair by using Tophat2 mapper tool */ process mapping { - + input: - file 'genome.index.fa' from genome_file + file 'genome.index.fa' from genome_file file genome_index from genome_index set pair_id, file(read1), file(read2) from read_pairs - + output: set pair_id, "tophat_out/accepted_hits.bam" into bam - + """ tophat2 -p ${task.cpus} genome.index ${read1} ${read2} """ @@ -66,16 +66,17 @@ process mapping { * Step 3. Assembles the transcript by using the "cufflinks" tool */ process makeTranscript { - + input: - file annot from annotation_file + file annot from annotation_file set pair_id, file(bam_file) from bam - + output: set pair_id, file('transcript_*.gtf') into transcripts - + """ cufflinks --no-update-check -q -p ${task.cpus} -G $annot ${bam_file} mv transcripts.gtf transcript_${pair_id}.gtf + """ } diff --git a/rna-ex6.nf b/rna-ex6.nf index de814e3..d7c6f8a 100644 --- a/rna-ex6.nf +++ b/rna-ex6.nf @@ -5,9 +5,9 @@ params.reads = "$baseDir/data/ggal/reads/ggal_gut_{1,2}.fq" params.annot = "$baseDir/data/ggal/annotation.gff" params.genome = "$baseDir/data/ggal/genome.fa" - -/* - * prints user convenience +params.outdir = 'results' +/* + * prints user convenience */ println "R N A T O Y P I P E L I N E " println "=================================" @@ -21,18 +21,18 @@ println "reads : ${params.reads}" */ genome_file = file(params.genome) annotation_file = file(params.annot) - + /* * Step 1. Builds the genome index required by the mapping process */ process buildIndex { - + input: file genome from genome_file - + output: file 'genome.index*' into genome_index - + """ bowtie2-build --threads ${task.cpus} ${genome} genome.index """ @@ -40,7 +40,7 @@ process buildIndex { /* * Create the `read_pairs` channel that emits tuples containing three elements: - * the pair ID, the first read-pair file and the second read-pair file + * the pair ID, the first read-pair file and the second read-pair file */ read_pairs = Channel.fromFilePairs(params.reads, flat: true) @@ -48,15 +48,15 @@ read_pairs = Channel.fromFilePairs(params.reads, flat: true) * Step 2. Maps each read-pair by using Tophat2 mapper tool */ process mapping { - + input: - file 'genome.index.fa' from genome_file + file 'genome.index.fa' from genome_file file genome_index from genome_index set pair_id, file(read1), file(read2) from read_pairs - + output: set pair_id, "tophat_out/accepted_hits.bam" into bam - + """ tophat2 -p ${task.cpus} genome.index ${read1} ${read2} """ @@ -66,19 +66,17 @@ process mapping { * Step 3. Assembles the transcript by using the "cufflinks" tool */ process makeTranscript { - publishDir "results", mode: 'copy' - + publishDir params.outdir, mode: 'copy' + input: - file annot from annotation_file + file annot from annotation_file set pair_id, file(bam_file) from bam - + output: set pair_id, file('transcript_*.gtf') into transcripts - + """ cufflinks --no-update-check -q -p ${task.cpus} -G $annot ${bam_file} mv transcripts.gtf transcript_${pair_id}.gtf """ } - - diff --git a/rna-ex7.nf b/rna-ex7.nf index 62fd238..28eeab1 100644 --- a/rna-ex7.nf +++ b/rna-ex7.nf @@ -7,8 +7,8 @@ params.annot = "$baseDir/data/ggal/annotation.gff" params.genome = "$baseDir/data/ggal/genome.fa" params.outdir = 'results' -/* - * prints user convenience +/* + * prints user convenience */ println "R N A T O Y P I P E L I N E " println "=================================" @@ -22,19 +22,19 @@ println "reads : ${params.reads}" */ genome_file = file(params.genome) annotation_file = file(params.annot) - + /* * Step 1. Builds the genome index required by the mapping process */ process buildIndex { tag "$genome_file.baseName" - + input: file genome from genome_file - + output: file 'genome.index*' into genome_index - + """ bowtie2-build --threads ${task.cpus} ${genome} genome.index """ @@ -42,7 +42,7 @@ process buildIndex { /* * Create the `read_pairs` channel that emits tuples containing three elements: - * the pair ID, the first read-pair file and the second read-pair file + * the pair ID, the first read-pair file and the second read-pair file */ read_pairs = Channel.fromFilePairs(params.reads, flat: true) @@ -51,15 +51,15 @@ read_pairs = Channel.fromFilePairs(params.reads, flat: true) */ process mapping { tag "$pair_id" - + input: - file 'genome.index.fa' from genome_file + file 'genome.index.fa' from genome_file file genome_index from genome_index set pair_id, file(read1), file(read2) from read_pairs - + output: set pair_id, "tophat_out/accepted_hits.bam" into bam - + """ tophat2 -p ${task.cpus} genome.index ${read1} ${read2} """ @@ -68,24 +68,18 @@ process mapping { /* * Step 3. Assembles the transcript by using the "cufflinks" tool */ -process makeTranscript { - tag "$pair_id" - publishDir params.outdir, mode: 'copy' - - input: - file annot from annotation_file - set pair_id, file(bam_file) from bam - - output: - set pair_id, file('transcript_*.gtf') into transcripts - - """ - cufflinks --no-update-check -q -p ${task.cpus} -G $annot ${bam_file} - mv transcripts.gtf transcript_${pair_id}.gtf - """ -} + process makeTranscript { + tag "$pair_id" + publishDir params.outdir, mode: 'copy' -workflow.onComplete { - println ( workflow.success ? "Done!" : "Oops .. something went wrong" ) -} + input: + file annot from annotation_file + set pair_id, file(bam_file) from bam + + output: + set pair_id, file('transcript_*.gtf') into transcripts + """ + quantify.sh $annot $bam_file $pair_id + """ + }