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Merge pull request #1 from FranBonath/FB
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mods_crg-course_nov16
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@FranBonath
FranBonath authored Aug 7, 2018
2 parents b19ea7a + 795ec1a commit 77bdcd7
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Showing 18 changed files with 443 additions and 95 deletions.
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10 changes: 10 additions & 0 deletions bin/quantify.sh
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#!/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
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57 changes: 57 additions & 0 deletions my_transcripts/transcript_ggal_gut.gtf
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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";
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