# /gscratch/srlab/programs/stringtie-1.3.6.Linux_x86_64/stringtie Geoduck-juvenile-OA-exposure-RNA-EPI-115-1.sorted.bam -p 28 -o Geoduck-juvenile-OA-exposure-RNA-EPI-115-1.gtf -G /gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v070_genome_snap02.all.renamed.putative_function.domain_added.gff -C Geoduck-juvenile-OA-exposure-RNA-EPI-115-1.cov_refs.gtf # StringTie version 1.3.6 PGA_scaffold1__77_contigs__length_89643857 StringTie transcript 59518592 59518806 1000 . . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "9.409303"; FPKM "28456.729557"; TPM "59514.580005"; PGA_scaffold1__77_contigs__length_89643857 StringTie exon 59518592 59518806 1000 . . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "9.409303"; PGA_scaffold2__36_contigs__length_69596280 StringTie transcript 34077070 34077401 1000 . . gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "3.138554"; FPKM "9491.987066"; TPM "19851.600393"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 34077070 34077401 1000 . . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "3.138554"; PGA_scaffold2__36_contigs__length_69596280 StringTie transcript 56820904 56821147 1000 . . gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "8.598361"; FPKM "26004.182628"; TPM "54385.308205"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 56820904 56821147 1000 . . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "8.598361"; PGA_scaffold3__111_contigs__length_57743597 StringTie transcript 4637780 4638023 1000 . . gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "9.934426"; FPKM "30044.868784"; TPM "62836.024196"; PGA_scaffold3__111_contigs__length_57743597 StringTie exon 4637780 4638023 1000 . . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "9.934426"; PGA_scaffold3__111_contigs__length_57743597 StringTie transcript 20818885 20822517 1000 - . gene_id "STRG.5"; transcript_id "STRG.5.1"; cov "5.024242"; FPKM "15194.908254"; TPM "31778.724999"; PGA_scaffold3__111_contigs__length_57743597 StringTie exon 20818885 20818931 1000 - . gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "1"; cov "6.000000"; PGA_scaffold3__111_contigs__length_57743597 StringTie exon 20821412 20821546 1000 - . gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "2"; cov "4.711111"; PGA_scaffold3__111_contigs__length_57743597 StringTie exon 20822370 20822517 1000 - . gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "3"; cov "5.000000"; PGA_scaffold4__129_contigs__length_65288255 StringTie transcript 10443579 10444210 1000 + . gene_id "STRG.6"; transcript_id "STRG.6.1"; cov "2.527660"; FPKM "7644.449013"; TPM "15987.647894"; PGA_scaffold4__129_contigs__length_65288255 StringTie exon 10443579 10443667 1000 + . gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "1"; cov "2.044944"; PGA_scaffold4__129_contigs__length_65288255 StringTie exon 10444065 10444210 1000 + . gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "2"; cov "2.821918"; PGA_scaffold5__109_contigs__length_67248332 StringTie transcript 12247649 12247873 1000 . . gene_id "STRG.7"; transcript_id "STRG.7.1"; cov "9.364445"; FPKM "28321.064676"; TPM "59230.849634"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 12247649 12247873 1000 . . gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "1"; cov "9.364445"; PGA_scaffold5__109_contigs__length_67248332 StringTie transcript 11821793 11827300 1000 + . gene_id "STRG.8"; transcript_id "STRG.8.1"; cov "2.912903"; FPKM "8809.546562"; TPM "18424.340107"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 11821793 11821814 1000 + . gene_id "STRG.8"; transcript_id "STRG.8.1"; exon_number "1"; cov "3.000000"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 11823212 11823273 1000 + . gene_id "STRG.8"; transcript_id "STRG.8.1"; exon_number "2"; cov "3.000000"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 11826265 11826361 1000 + . gene_id "STRG.8"; transcript_id "STRG.8.1"; exon_number "3"; cov "2.721649"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 11827172 11827300 1000 + . gene_id "STRG.8"; transcript_id "STRG.8.1"; exon_number "4"; cov "3.000000"; PGA_scaffold8__63_contigs__length_61151155 StringTie transcript 23684475 23686250 1000 + . gene_id "STRG.9"; transcript_id "STRG.9.1"; cov "3.640625"; FPKM "11010.409702"; TPM "23027.238875"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 23684475 23684576 1000 + . gene_id "STRG.9"; transcript_id "STRG.9.1"; exon_number "1"; cov "3.598039"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 23685072 23685122 1000 + . gene_id "STRG.9"; transcript_id "STRG.9.1"; exon_number "2"; cov "5.215686"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 23686084 23686250 1000 + . gene_id "STRG.9"; transcript_id "STRG.9.1"; exon_number "3"; cov "3.185629"; PGA_scaffold8__63_contigs__length_61151155 StringTie transcript 34748509 34748783 1000 . . gene_id "STRG.10"; transcript_id "STRG.10.1"; cov "8.778182"; FPKM "26548.018613"; TPM "55522.690144"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 34748509 34748783 1000 . . gene_id "STRG.10"; transcript_id "STRG.10.1"; exon_number "1"; cov "8.778182"; PGA_scaffold8__63_contigs__length_61151155 StringTie transcript 55813352 55816012 1000 + . gene_id "STRG.11"; transcript_id "STRG.11.1"; cov "6.782805"; FPKM "20513.362948"; TPM "42901.774003"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 55813352 55813430 1000 + . gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "1"; cov "5.455696"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 55814325 55814372 1000 + . gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "2"; cov "10.000000"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 55814659 55814706 1000 + . gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "3"; cov "7.458333"; PGA_scaffold8__63_contigs__length_61151155 StringTie exon 55815967 55816012 1000 + . gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "4"; cov "5.000000"; PGA_scaffold10__49_contigs__length_53961475 StringTie transcript 11892156 11897551 1000 - . gene_id "STRG.12"; transcript_id "STRG.12.1"; cov "2.791139"; FPKM "8441.293439"; TPM "17654.173250"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 11892156 11892295 1000 - . gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "1"; cov "1.235714"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 11894140 11894260 1000 - . gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "2"; cov "4.231405"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 11897497 11897551 1000 - . gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "3"; cov "3.581818"; PGA_scaffold10__49_contigs__length_53961475 StringTie transcript 37153301 37153500 1000 . . gene_id "STRG.13"; transcript_id "STRG.13.1"; cov "3.760000"; FPKM "11371.437729"; TPM "23782.295120"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 37153301 37153500 1000 . . gene_id "STRG.13"; transcript_id "STRG.13.1"; exon_number "1"; cov "3.760000"; PGA_scaffold10__49_contigs__length_53961475 StringTie transcript 38740504 38740961 1000 . . gene_id "STRG.14"; transcript_id "STRG.14.1"; cov "3.604804"; FPKM "10902.075588"; TPM "22800.668239"; PGA_scaffold10__49_contigs__length_53961475 StringTie exon 38740504 38740961 1000 . . gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "1"; cov "3.604804"; PGA_scaffold12__71_contigs__length_50438331 StringTie transcript 28628032 28628368 1000 + . gene_id "STRG.15"; transcript_id "STRG.15.1"; cov "7.931751"; FPKM "23988.141642"; TPM "50168.947633"; PGA_scaffold12__71_contigs__length_50438331 StringTie exon 28628032 28628368 1000 + . gene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; cov "7.931751"; PGA_scaffold13__52_contigs__length_44396874 StringTie transcript 40778170 40778413 1000 . . gene_id "STRG.16"; transcript_id "STRG.16.1"; cov "14.823771"; FPKM "44831.805540"; TPM "93761.515083"; PGA_scaffold13__52_contigs__length_44396874 StringTie exon 40778170 40778413 1000 . . gene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; cov "14.823771"; PGA_scaffold13__52_contigs__length_44396874 StringTie transcript 42168004 42168227 1000 . . gene_id "STRG.17"; transcript_id "STRG.17.1"; cov "2.660714"; FPKM "8046.846693"; TPM "16829.224888"; PGA_scaffold13__52_contigs__length_44396874 StringTie exon 42168004 42168227 1000 . . gene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "2.660714"; PGA_scaffold14__91_contigs__length_45393038 StringTie transcript 13477023 13481506 1000 - . gene_id "STRG.18"; transcript_id "STRG.18.1"; cov "2.539162"; FPKM "7679.234725"; TPM "16060.398947"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 13477023 13477105 1000 - . gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; cov "1.333333"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 13477965 13478056 1000 - . gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "2"; cov "2.108696"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 13479552 13479653 1000 - . gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "3"; cov "3.320261"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 13481418 13481506 1000 - . gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "4"; cov "3.213483"; PGA_scaffold15__101_contigs__length_47938513 StringTie transcript 39318730 39320793 1000 + . gene_id "STRG.19"; transcript_id "STRG.19.1"; cov "3.282609"; FPKM "9927.655274"; TPM "20762.759575"; PGA_scaffold15__101_contigs__length_47938513 StringTie exon 39318730 39318767 1000 + . gene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "1.157895"; PGA_scaffold15__101_contigs__length_47938513 StringTie exon 39320003 39320123 1000 + . gene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "2"; cov "3.917355"; PGA_scaffold15__101_contigs__length_47938513 StringTie exon 39320723 39320793 1000 + . gene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "3"; cov "3.338028"; PGA_scaffold14__91_contigs__length_45393038 StringTie transcript 30442228 30442444 1000 . . gene_id "STRG.20"; transcript_id "STRG.20.1"; cov "2.760369"; FPKM "8348.235157"; TPM "17459.550585"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 30442228 30442444 1000 . . gene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "2.760369"; PGA_scaffold15__101_contigs__length_47938513 StringTie transcript 21427849 21428057 1000 . . gene_id "STRG.21"; transcript_id "STRG.21.1"; cov "2.870813"; FPKM "8682.252995"; TPM "18158.117553"; PGA_scaffold15__101_contigs__length_47938513 StringTie exon 21427849 21428057 1000 . . gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; cov "2.870813"; PGA_scaffold16__33_contigs__length_31980953 StringTie transcript 17758152 17758389 1000 . . gene_id "STRG.22"; transcript_id "STRG.22.1"; cov "3.130252"; FPKM "9466.879174"; TPM "19799.089591"; PGA_scaffold16__33_contigs__length_31980953 StringTie exon 17758152 17758389 1000 . . gene_id "STRG.22"; transcript_id "STRG.22.1"; exon_number "1"; cov "3.130252"; PGA_scaffold17__51_contigs__length_34923512 StringTie transcript 9072182 9072440 1000 . . gene_id "STRG.23"; transcript_id "STRG.23.1"; cov "5.239382"; FPKM "15845.560146"; TPM "33139.502386"; PGA_scaffold17__51_contigs__length_34923512 StringTie exon 9072182 9072440 1000 . . gene_id "STRG.23"; transcript_id "STRG.23.1"; exon_number "1"; cov "5.239382"; PGA_scaffold456__1_contigs__length_65608 StringTie transcript 15510 16721 1000 - . gene_id "STRG.24"; transcript_id "STRG.24.1"; cov "2.813084"; FPKM "8507.662109"; TPM "17792.977097"; PGA_scaffold456__1_contigs__length_65608 StringTie exon 15510 15594 1000 - . gene_id "STRG.24"; transcript_id "STRG.24.1"; exon_number "1"; cov "2.517647"; PGA_scaffold456__1_contigs__length_65608 StringTie exon 16593 16721 1000 - . gene_id "STRG.24"; transcript_id "STRG.24.1"; exon_number "2"; cov "3.007752"; PGA_scaffold17589__1_contigs__length_5167 StringTie transcript 1285 2431 1000 + . gene_id "STRG.25"; transcript_id "STRG.25.1"; reference_id "PGEN_00031885-RA"; ref_gene_id "PGEN_00031885"; cov "0.217960"; FPKM "659.180470"; TPM "1378.614108"; PGA_scaffold17589__1_contigs__length_5167 StringTie exon 1285 2431 1000 + . gene_id "STRG.25"; transcript_id "STRG.25.1"; exon_number "1"; reference_id "PGEN_00031885-RA"; ref_gene_id "PGEN_00031885"; cov "0.217960"; PGA_scaffold34826__1_contigs__length_1153 StringTie transcript 63 272 1000 . . gene_id "STRG.26"; transcript_id "STRG.26.1"; cov "4.566667"; FPKM "13811.055696"; TPM "28884.527210"; PGA_scaffold34826__1_contigs__length_1153 StringTie exon 63 272 1000 . . gene_id "STRG.26"; transcript_id "STRG.26.1"; exon_number "1"; cov "4.566667"; PGA_scaffold51392__1_contigs__length_1221 StringTie transcript 1 451 1000 . . gene_id "STRG.27"; transcript_id "STRG.27.1"; cov "3.977827"; FPKM "12030.215964"; TPM "25160.067992"; PGA_scaffold51392__1_contigs__length_1221 StringTie exon 1 451 1000 . . gene_id "STRG.27"; transcript_id "STRG.27.1"; exon_number "1"; cov "3.977827"; PGA_scaffold58221__1_contigs__length_14877 StringTie transcript 5252 6022 1000 - . gene_id "STRG.28"; transcript_id "STRG.28.1"; reference_id "PGEN_00017195-RA"; ref_gene_id "PGEN_00017195"; cov "0.195850"; FPKM "592.312787"; TPM "1238.766622"; PGA_scaffold58221__1_contigs__length_14877 StringTie exon 5252 6022 1000 - . gene_id "STRG.28"; transcript_id "STRG.28.1"; exon_number "1"; reference_id "PGEN_00017195-RA"; ref_gene_id "PGEN_00017195"; cov "0.195850"; PGA_scaffold59822__1_contigs__length_1640 StringTie transcript 949 1620 1000 - . gene_id "STRG.29"; transcript_id "STRG.29.1"; reference_id "PGEN_00047643-RA"; ref_gene_id "PGEN_00047643"; cov "0.449405"; FPKM "1359.143876"; TPM "2842.521898"; PGA_scaffold59822__1_contigs__length_1640 StringTie exon 949 1620 1000 - . gene_id "STRG.29"; transcript_id "STRG.29.1"; exon_number "1"; reference_id "PGEN_00047643-RA"; ref_gene_id "PGEN_00047643"; cov "0.449405"; PGA_scaffold66031__1_contigs__length_24994 StringTie transcript 1589 2290 1000 + . gene_id "STRG.30"; transcript_id "STRG.30.1"; reference_id "PGEN_00012761-RA"; ref_gene_id "PGEN_00012761"; cov "1.267806"; FPKM "3834.249197"; TPM "8018.972459"; PGA_scaffold66031__1_contigs__length_24994 StringTie exon 1589 2290 1000 + . gene_id "STRG.30"; transcript_id "STRG.30.1"; exon_number "1"; reference_id "PGEN_00012761-RA"; ref_gene_id "PGEN_00012761"; cov "1.267806"; PGA_scaffold121507__1_contigs__length_13142 StringTie transcript 3368 4568 1000 + . gene_id "STRG.31"; transcript_id "STRG.31.1"; reference_id "PGEN_00018657-RA"; ref_gene_id "PGEN_00018657"; cov "0.322650"; FPKM "975.796378"; TPM "2040.786575"; PGA_scaffold121507__1_contigs__length_13142 StringTie exon 3368 3499 1000 + . gene_id "STRG.31"; transcript_id "STRG.31.1"; exon_number "1"; reference_id "PGEN_00018657-RA"; ref_gene_id "PGEN_00018657"; cov "0.765152"; PGA_scaffold121507__1_contigs__length_13142 StringTie exon 4233 4568 1000 + . gene_id "STRG.31"; transcript_id "STRG.31.1"; exon_number "2"; reference_id "PGEN_00018657-RA"; ref_gene_id "PGEN_00018657"; cov "0.148810"; PGA_scaffold224405__1_contigs__length_1297 StringTie transcript 66 277 1000 . . gene_id "STRG.32"; transcript_id "STRG.32.1"; cov "3.205189"; FPKM "9693.512532"; TPM "20273.071998"; PGA_scaffold224405__1_contigs__length_1297 StringTie exon 66 277 1000 . . gene_id "STRG.32"; transcript_id "STRG.32.1"; exon_number "1"; cov "3.205189"; PGA_scaffold224403__1_contigs__length_1297 StringTie transcript 1021 1232 1000 + . gene_id "STRG.33"; transcript_id "STRG.33.1"; cov "3.205189"; FPKM "9693.512532"; TPM "20273.071998"; PGA_scaffold224403__1_contigs__length_1297 StringTie exon 1021 1232 1000 + . gene_id "STRG.33"; transcript_id "STRG.33.1"; exon_number "1"; cov "3.205189"; PGA_scaffold247109__1_contigs__length_1297 StringTie transcript 1021 1232 1000 . . gene_id "STRG.34"; transcript_id "STRG.34.1"; cov "3.205189"; FPKM "9693.512532"; TPM "20273.071998"; PGA_scaffold247109__1_contigs__length_1297 StringTie exon 1021 1232 1000 . . gene_id "STRG.34"; transcript_id "STRG.34.1"; exon_number "1"; cov "3.205189"; PGA_scaffold247111__1_contigs__length_1297 StringTie transcript 66 277 1000 - . gene_id "STRG.35"; transcript_id "STRG.35.1"; cov "3.205189"; FPKM "9693.512532"; TPM "20273.071998"; PGA_scaffold247111__1_contigs__length_1297 StringTie exon 66 277 1000 - . gene_id "STRG.35"; transcript_id "STRG.35.1"; exon_number "1"; cov "3.205189"; PGA_scaffold313645__2_contigs__length_2213805 StringTie transcript 595018 595269 1000 . . gene_id "STRG.36"; transcript_id "STRG.36.1"; cov "4.698413"; FPKM "14209.497567"; TPM "29717.831000"; PGA_scaffold313645__2_contigs__length_2213805 StringTie exon 595018 595269 1000 . . gene_id "STRG.36"; transcript_id "STRG.36.1"; exon_number "1"; cov "4.698413";