# /gscratch/srlab/programs/stringtie-1.3.6.Linux_x86_64/stringtie Geoduck-ctenidia-RNA-7.sorted.bam -p 28 -o Geoduck-ctenidia-RNA-7.gtf -G /gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v070_genome_snap02.all.renamed.putative_function.domain_added.gff -C Geoduck-ctenidia-RNA-7.cov_refs.gtf # StringTie version 1.3.6 PGA_scaffold1__77_contigs__length_89643857 StringTie transcript 19804338 19804679 1000 . . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "2.877193"; FPKM "13839.012622"; TPM "24373.988063"; PGA_scaffold1__77_contigs__length_89643857 StringTie exon 19804338 19804679 1000 . . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "2.877193"; PGA_scaffold2__36_contigs__length_69596280 StringTie transcript 28117077 28117550 1000 . . gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "3.472574"; FPKM "16702.736110"; TPM "29417.726660"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28117077 28117550 1000 . . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "3.472574"; PGA_scaffold2__36_contigs__length_69596280 StringTie transcript 28120890 28121426 1000 - . gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "2.814697"; FPKM "13538.413068"; TPM "23844.556510"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28120890 28120958 1000 - . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "1.318841"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28121183 28121426 1000 - . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "3.237705"; PGA_scaffold2__36_contigs__length_69596280 StringTie transcript 28127311 28130358 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "3.523952"; FPKM "16949.859189"; TPM "29852.972665"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28127311 28127406 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "3.710938"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28127587 28127704 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "4.760593"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28129446 28129533 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "3"; cov "2.215909"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28130327 28130358 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "4"; cov "2.000000"; PGA_scaffold2__36_contigs__length_69596280 StringTie transcript 28144448 28146737 1000 - . gene_id "STRG.5"; transcript_id "STRG.5.1"; cov "7.878290"; FPKM "37893.792579"; TPM "66740.516334"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28144448 28144474 1000 - . gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "1"; cov "4.000000"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28145001 28145144 1000 - . gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "2"; cov "10.083333"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28146605 28146737 1000 - . gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "3"; cov "6.278195"; PGA_scaffold3__111_contigs__length_57743597 StringTie transcript 15221110 15223374 1000 + . gene_id "STRG.6"; transcript_id "STRG.6.1"; cov "3.909091"; FPKM "18802.339534"; TPM "33115.657299"; PGA_scaffold3__111_contigs__length_57743597 StringTie exon 15221110 15221210 1000 + . gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "1"; cov "3.623762"; PGA_scaffold3__111_contigs__length_57743597 StringTie exon 15223245 15223374 1000 + . gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "2"; cov "4.130769"; PGA_scaffold4__129_contigs__length_65288255 StringTie transcript 47021044 47021315 1000 . . gene_id "STRG.7"; transcript_id "STRG.7.1"; cov "4.426471"; FPKM "21290.885958"; TPM "37498.614557"; PGA_scaffold4__129_contigs__length_65288255 StringTie exon 47021044 47021315 1000 . . gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "1"; cov "4.426471"; PGA_scaffold5__109_contigs__length_67248332 StringTie transcript 25648097 25648478 1000 . . gene_id "STRG.8"; transcript_id "STRG.8.1"; cov "4.400524"; FPKM "21166.083464"; TPM "37278.805921"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 25648097 25648478 1000 . . gene_id "STRG.8"; transcript_id "STRG.8.1"; exon_number "1"; cov "4.400524"; PGA_scaffold5__109_contigs__length_67248332 StringTie transcript 25648574 25649252 1000 . . gene_id "STRG.9"; transcript_id "STRG.9.1"; cov "3.664212"; FPKM "17624.495861"; TPM "31041.177824"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 25648574 25649252 1000 . . gene_id "STRG.9"; transcript_id "STRG.9.1"; exon_number "1"; cov "3.664212"; PGA_scaffold5__109_contigs__length_67248332 StringTie transcript 60424516 60429078 1000 - . gene_id "STRG.10"; transcript_id "STRG.10.1"; cov "4.578475"; FPKM "22022.010104"; TPM "38786.308390"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 60424516 60424682 1000 - . gene_id "STRG.10"; transcript_id "STRG.10.1"; exon_number "1"; cov "5.089820"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 60429023 60429078 1000 - . gene_id "STRG.10"; transcript_id "STRG.10.1"; exon_number "2"; cov "3.053571"; PGA_scaffold7__69_contigs__length_43120122 StringTie transcript 4967465 4967679 1000 . . gene_id "STRG.11"; transcript_id "STRG.11.1"; cov "2.790698"; FPKM "13422.980261"; TPM "23641.250253"; PGA_scaffold7__69_contigs__length_43120122 StringTie exon 4967465 4967679 1000 . . gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "1"; cov "2.790698"; PGA_scaffold7__69_contigs__length_43120122 StringTie transcript 34173420 34173653 1000 . . gene_id "STRG.12"; transcript_id "STRG.12.1"; cov "2.581197"; FPKM "12415.301255"; TPM "21866.473631"; PGA_scaffold7__69_contigs__length_43120122 StringTie exon 34173420 34173653 1000 . . gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "1"; cov "2.581197"; PGA_scaffold8__63_contigs__length_61151155 StringTie transcript 25347338 25347569 1000 . . gene_id "STRG.13"; transcript_id "STRG.13.1"; cov "2.603448"; FPKM "12522.326355"; TPM "22054.971798"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 25347338 25347569 1000 . . gene_id "STRG.13"; transcript_id "STRG.13.1"; exon_number "1"; cov "2.603448"; PGA_scaffold8__63_contigs__length_61151155 StringTie transcript 51282096 51282485 1000 . . gene_id "STRG.14"; transcript_id "STRG.14.1"; cov "4.184616"; FPKM "20127.587424"; TPM "35449.752738"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 51282096 51282485 1000 . . gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "1"; cov "4.184616"; PGA_scaffold8__63_contigs__length_61151155 StringTie transcript 59459419 59459642 1000 . . gene_id "STRG.15"; transcript_id "STRG.15.1"; cov "4.031250"; FPKM "19389.912193"; TPM "34150.520795"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 59459419 59459642 1000 . . gene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; cov "4.031250"; PGA_scaffold9__45_contigs__length_38581958 StringTie transcript 35335713 35335939 1000 . . gene_id "STRG.16"; transcript_id "STRG.16.1"; cov "3.929515"; FPKM "18900.576946"; TPM "33288.678132"; PGA_scaffold9__45_contigs__length_38581958 StringTie exon 35335713 35335939 1000 . . gene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; cov "3.929515"; PGA_scaffold10__49_contigs__length_53961475 StringTie transcript 25488386 25494715 1000 + . gene_id "STRG.17"; transcript_id "STRG.17.1"; cov "3.477583"; FPKM "16726.828903"; TPM "29460.160138"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 25488386 25488601 1000 + . gene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "3.837963"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 25492178 25492324 1000 + . gene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "2"; cov "4.017007"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 25493927 25494052 1000 + . gene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "3"; cov "2.750000"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 25494692 25494715 1000 + . gene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "4"; cov "0.750000"; PGA_scaffold10__49_contigs__length_53961475 StringTie transcript 38010243 38010461 1000 . . gene_id "STRG.18"; transcript_id "STRG.18.1"; cov "2.748858"; FPKM "13221.734016"; TPM "23286.804909"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 38010243 38010461 1000 . . gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; cov "2.748858"; PGA_scaffold10__49_contigs__length_53961475 StringTie transcript 41639338 41639586 1000 . . gene_id "STRG.19"; transcript_id "STRG.19.1"; cov "3.032129"; FPKM "14584.239397"; TPM "25686.520178"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 41639338 41639586 1000 . . gene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "3.032129"; PGA_scaffold9__45_contigs__length_38581958 StringTie transcript 9729217 9739573 1000 + . gene_id "STRG.20"; transcript_id "STRG.20.1"; cov "2.856164"; FPKM "13737.865221"; TPM "24195.842003"; PGA_scaffold9__45_contigs__length_38581958 StringTie exon 9729217 9729240 1000 + . gene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "2.000000"; PGA_scaffold9__45_contigs__length_38581958 StringTie exon 9738908 9739004 1000 + . gene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "2"; cov "2.061856"; PGA_scaffold9__45_contigs__length_38581958 StringTie exon 9739176 9739236 1000 + . gene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "3"; cov "3.147541"; PGA_scaffold9__45_contigs__length_38581958 StringTie exon 9739464 9739573 1000 + . gene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "4"; cov "3.581818"; PGA_scaffold12__71_contigs__length_50438331 StringTie transcript 44176284 44176547 1000 . . gene_id "STRG.21"; transcript_id "STRG.21.1"; cov "3.958333"; FPKM "19039.188664"; TPM "33532.808293"; PGA_scaffold12__71_contigs__length_50438331 StringTie exon 44176284 44176547 1000 . . gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; cov "3.958333"; PGA_scaffold14__91_contigs__length_45393038 StringTie transcript 20551162 20552516 1000 - . gene_id "STRG.22"; transcript_id "STRG.22.1"; cov "2.995025"; FPKM "14405.772841"; TPM "25372.195608"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 20551162 20551292 1000 - . gene_id "STRG.22"; transcript_id "STRG.22.1"; exon_number "1"; cov "3.236641"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 20552447 20552516 1000 - . gene_id "STRG.22"; transcript_id "STRG.22.1"; exon_number "2"; cov "2.542857"; PGA_scaffold14__91_contigs__length_45393038 StringTie transcript 30461661 30462640 1000 . . gene_id "STRG.23"; transcript_id "STRG.23.1"; cov "5.774490"; FPKM "27774.723488"; TPM "48918.286096"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 30461661 30462640 1000 . . gene_id "STRG.23"; transcript_id "STRG.23.1"; exon_number "1"; cov "5.774490"; PGA_scaffold31947__1_contigs__length_11664 StringTie transcript 2861 3067 1000 . . gene_id "STRG.24"; transcript_id "STRG.24.1"; cov "2.917874"; FPKM "14034.684193"; TPM "24718.614999"; PGA_scaffold31947__1_contigs__length_11664 StringTie exon 2861 3067 1000 . . gene_id "STRG.24"; transcript_id "STRG.24.1"; exon_number "1"; cov "2.917874"; PGA_scaffold34826__1_contigs__length_1153 StringTie transcript 1 213 1000 . . gene_id "STRG.25"; transcript_id "STRG.25.1"; cov "7.845070"; FPKM "37734.007678"; TPM "66459.094864"; PGA_scaffold34826__1_contigs__length_1153 StringTie exon 1 213 1000 . . gene_id "STRG.25"; transcript_id "STRG.25.1"; exon_number "1"; cov "7.845070"; PGA_scaffold50183__1_contigs__length_7081 StringTie transcript 603 839 1000 . . gene_id "STRG.26"; transcript_id "STRG.26.1"; cov "2.540084"; FPKM "12217.551808"; TPM "21518.187030"; PGA_scaffold50183__1_contigs__length_7081 StringTie exon 603 839 1000 . . gene_id "STRG.26"; transcript_id "STRG.26.1"; exon_number "1"; cov "2.540084"; PGA_scaffold51392__1_contigs__length_1221 StringTie transcript 108 329 1000 . . gene_id "STRG.27"; transcript_id "STRG.27.1"; cov "5.225225"; FPKM "25132.813381"; TPM "44265.216749"; PGA_scaffold51392__1_contigs__length_1221 StringTie exon 108 329 1000 . . gene_id "STRG.27"; transcript_id "STRG.27.1"; exon_number "1"; cov "5.225225"; PGA_scaffold51828__1_contigs__length_8816 StringTie transcript 1426 1651 1000 . . gene_id "STRG.28"; transcript_id "STRG.28.1"; cov "2.672566"; FPKM "12854.777072"; TPM "22640.501273"; PGA_scaffold51828__1_contigs__length_8816 StringTie exon 1426 1651 1000 . . gene_id "STRG.28"; transcript_id "STRG.28.1"; exon_number "1"; cov "2.672566"; PGA_scaffold66377__1_contigs__length_3789 StringTie transcript 3257 3762 1000 - . gene_id "STRG.29"; transcript_id "STRG.29.1"; reference_id "PGEN_00036744-RA"; ref_gene_id "PGEN_00036744"; cov "1.051383"; FPKM "5057.047827"; TPM "8906.735381"; PGA_scaffold66377__1_contigs__length_3789 StringTie exon 3257 3762 1000 - . gene_id "STRG.29"; transcript_id "STRG.29.1"; exon_number "1"; reference_id "PGEN_00036744-RA"; ref_gene_id "PGEN_00036744"; cov "1.051383"; PGA_scaffold70145__1_contigs__length_1661 StringTie transcript 55 1635 1000 + . gene_id "STRG.30"; transcript_id "STRG.30.1"; reference_id "PGEN_00047475-RA"; ref_gene_id "PGEN_00047475"; cov "2.453552"; FPKM "11801.341480"; TPM "20785.135776"; PGA_scaffold70145__1_contigs__length_1661 StringTie exon 55 382 1000 + . gene_id "STRG.30"; transcript_id "STRG.30.1"; exon_number "1"; reference_id "PGEN_00047475-RA"; ref_gene_id "PGEN_00047475"; cov "2.609756"; PGA_scaffold70145__1_contigs__length_1661 StringTie exon 1598 1635 1000 + . gene_id "STRG.30"; transcript_id "STRG.30.1"; exon_number "2"; reference_id "PGEN_00047475-RA"; ref_gene_id "PGEN_00047475"; cov "1.105263"; PGA_scaffold313632__1_contigs__length_455018 StringTie transcript 116866 117110 1000 . . gene_id "STRG.31"; transcript_id "STRG.31.1"; cov "4.930612"; FPKM "23715.754106"; TPM "41769.418329"; PGA_scaffold313632__1_contigs__length_455018 StringTie exon 116866 117110 1000 . . gene_id "STRG.31"; transcript_id "STRG.31.1"; exon_number "1"; cov "4.930612";