# /gscratch/srlab/programs/stringtie-1.3.6.Linux_x86_64/stringtie Geoduck-juvenile-OA-exposure-RNA-EPI-116-7.sorted.bam -p 28 -o Geoduck-juvenile-OA-exposure-RNA-EPI-116-7.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-116-7.cov_refs.gtf # StringTie version 1.3.6 PGA_scaffold1__77_contigs__length_89643857 StringTie transcript 49652559 49652785 1000 . . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "2.651982"; FPKM "12778.172882"; TPM "39484.457429"; PGA_scaffold1__77_contigs__length_89643857 StringTie exon 49652559 49652785 1000 . . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "2.651982"; PGA_scaffold2__36_contigs__length_69596280 StringTie transcript 28117036 28117512 1000 . . gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "5.570230"; FPKM "26839.308084"; TPM "82933.258711"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28117036 28117512 1000 . . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "5.570230"; PGA_scaffold2__36_contigs__length_69596280 StringTie transcript 28116400 28116895 1000 - . gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "3.581967"; FPKM "17259.164497"; TPM "53330.687585"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28116400 28116601 1000 - . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "4.118812"; PGA_scaffold2__36_contigs__length_69596280 StringTie exon 28116854 28116895 1000 - . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "1.000000"; PGA_scaffold4__129_contigs__length_65288255 StringTie transcript 37170508 37172457 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "2.518828"; FPKM "12136.590536"; TPM "37501.972840"; PGA_scaffold4__129_contigs__length_65288255 StringTie exon 37170508 37170570 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "2.000000"; PGA_scaffold4__129_contigs__length_65288255 StringTie exon 37172079 37172231 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "2.810457"; PGA_scaffold4__129_contigs__length_65288255 StringTie exon 37172435 37172457 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "3"; cov "2.000000"; PGA_scaffold5__109_contigs__length_67248332 StringTie transcript 42400582 42400877 1000 . . gene_id "STRG.5"; transcript_id "STRG.5.1"; cov "3.054054"; FPKM "14715.495807"; TPM "45470.770596"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 42400582 42400877 1000 . . gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "1"; cov "3.054054"; PGA_scaffold5__109_contigs__length_67248332 StringTie transcript 62067758 62067986 1000 . . gene_id "STRG.6"; transcript_id "STRG.6.1"; cov "2.628821"; FPKM "12666.575117"; TPM "39139.621182"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 62067758 62067986 1000 . . gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "1"; cov "2.628821"; PGA_scaffold5__109_contigs__length_67248332 StringTie transcript 25648552 25684697 1000 - . gene_id "STRG.7"; transcript_id "STRG.7.1"; cov "6.218537"; FPKM "29963.076996"; TPM "92585.680990"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 25648552 25649320 1000 - . gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "1"; cov "6.361046"; PGA_scaffold5__109_contigs__length_67248332 StringTie exon 25684677 25684697 1000 - . gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "2"; cov "1.000000"; PGA_scaffold6__104_contigs__length_61759565 StringTie transcript 23941861 23942063 1000 . . gene_id "STRG.8"; transcript_id "STRG.8.1"; cov "2.965517"; FPKM "14288.893706"; TPM "44152.573336"; PGA_scaffold6__104_contigs__length_61759565 StringTie exon 23941861 23942063 1000 . . gene_id "STRG.8"; transcript_id "STRG.8.1"; exon_number "1"; cov "2.965517"; PGA_scaffold7__69_contigs__length_43120122 StringTie transcript 32989185 32989471 1000 . . gene_id "STRG.9"; transcript_id "STRG.9.1"; cov "3.139373"; FPKM "15126.592463"; TPM "46741.056150"; PGA_scaffold7__69_contigs__length_43120122 StringTie exon 32989185 32989471 1000 . . gene_id "STRG.9"; transcript_id "STRG.9.1"; exon_number "1"; cov "3.139373"; PGA_scaffold14__91_contigs__length_45393038 StringTie transcript 30461396 30461974 1000 . . gene_id "STRG.10"; transcript_id "STRG.10.1"; cov "4.523316"; FPKM "21794.911823"; TPM "67346.112469"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 30461396 30461974 1000 . . gene_id "STRG.10"; transcript_id "STRG.10.1"; exon_number "1"; cov "4.523316"; PGA_scaffold14__91_contigs__length_45393038 StringTie transcript 30443406 30446448 1000 - . gene_id "STRG.11"; transcript_id "STRG.11.1"; cov "3.128408"; FPKM "15073.759274"; TPM "46577.801997"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 30443406 30443627 1000 - . gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "1"; cov "2.687687"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 30446292 30446448 1000 - . gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "2"; cov "3.751592"; PGA_scaffold14__91_contigs__length_45393038 StringTie transcript 30462064 30466313 1000 - . gene_id "STRG.12"; transcript_id "STRG.12.1"; cov "2.774594"; FPKM "13368.960200"; TPM "41309.985767"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 30462064 30463035 1000 - . gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "1"; cov "2.844650"; PGA_scaffold14__91_contigs__length_45393038 StringTie exon 30466239 30466313 1000 - . gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "2"; cov "1.866667"; PGA_scaffold17__51_contigs__length_34923512 StringTie transcript 32760689 32761275 1000 . . gene_id "STRG.13"; transcript_id "STRG.13.1"; cov "3.073254"; FPKM "14808.008094"; TPM "45756.632862"; PGA_scaffold17__51_contigs__length_34923512 StringTie exon 32760689 32761275 1000 . . gene_id "STRG.13"; transcript_id "STRG.13.1"; exon_number "1"; cov "3.073254"; PGA_scaffold3541__1_contigs__length_1082 StringTie transcript 613 1082 1000 - . gene_id "STRG.14"; transcript_id "STRG.14.1"; reference_id "PGEN_00052174-RA"; ref_gene_id "PGEN_00052174"; cov "0.680180"; FPKM "3277.344126"; TPM "10126.968529"; PGA_scaffold3541__1_contigs__length_1082 StringTie exon 613 743 1000 - . gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "1"; reference_id "PGEN_00052174-RA"; ref_gene_id "PGEN_00052174"; cov "0.580153"; PGA_scaffold3541__1_contigs__length_1082 StringTie exon 992 1082 1000 - . gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "2"; reference_id "PGEN_00052174-RA"; ref_gene_id "PGEN_00052174"; cov "0.824176"; PGA_scaffold16133__1_contigs__length_2180 StringTie transcript 63 362 1000 + . gene_id "STRG.15"; transcript_id "STRG.15.1"; reference_id "PGEN_00044386-RA"; ref_gene_id "PGEN_00044386"; cov "0.866667"; FPKM "4175.903440"; TPM "12903.510004"; PGA_scaffold16133__1_contigs__length_2180 StringTie exon 63 362 1000 + . gene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; reference_id "PGEN_00044386-RA"; ref_gene_id "PGEN_00044386"; cov "0.866667"; PGA_scaffold18764__1_contigs__length_8798 StringTie transcript 4765 5202 1000 - . gene_id "STRG.16"; transcript_id "STRG.16.1"; reference_id "PGEN_00023780-RA"; ref_gene_id "PGEN_00023780"; cov "0.127854"; FPKM "616.045100"; TPM "1903.574692"; PGA_scaffold18764__1_contigs__length_8798 StringTie exon 4765 5202 1000 - . gene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; reference_id "PGEN_00023780-RA"; ref_gene_id "PGEN_00023780"; cov "0.127854"; PGA_scaffold20699__1_contigs__length_17598 StringTie transcript 11289 11581 1000 . . gene_id "STRG.17"; transcript_id "STRG.17.1"; cov "5.078498"; FPKM "24469.972052"; TPM "75612.028318"; PGA_scaffold20699__1_contigs__length_17598 StringTie exon 11289 11581 1000 . . gene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "5.078498"; PGA_scaffold40802__1_contigs__length_3857 StringTie transcript 957 3374 1000 + . gene_id "STRG.18"; transcript_id "STRG.18.1"; reference_id "PGEN_00036436-RA"; ref_gene_id "PGEN_00036436"; cov "1.560724"; FPKM "7520.111785"; TPM "23237.088463"; PGA_scaffold40802__1_contigs__length_3857 StringTie exon 957 1085 1000 + . gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; reference_id "PGEN_00036436-RA"; ref_gene_id "PGEN_00036436"; cov "1.333333"; PGA_scaffold40802__1_contigs__length_3857 StringTie exon 2144 2281 1000 + . gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "2"; reference_id "PGEN_00036436-RA"; ref_gene_id "PGEN_00036436"; cov "2.608696"; PGA_scaffold40802__1_contigs__length_3857 StringTie exon 3255 3374 1000 + . gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "3"; reference_id "PGEN_00036436-RA"; ref_gene_id "PGEN_00036436"; cov "0.600000"; PGA_scaffold43828__1_contigs__length_21394 StringTie transcript 14629 14854 1000 + . gene_id "STRG.19"; transcript_id "STRG.19.1"; cov "2.668142"; FPKM "12856.037390"; TPM "39725.058169"; PGA_scaffold43828__1_contigs__length_21394 StringTie exon 14629 14854 1000 + . gene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "2.668142"; PGA_scaffold51392__1_contigs__length_1221 StringTie transcript 1 307 1000 . . gene_id "STRG.20"; transcript_id "STRG.20.1"; cov "6.237785"; FPKM "30055.820563"; TPM "92872.257912"; PGA_scaffold51392__1_contigs__length_1221 StringTie exon 1 307 1000 . . gene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "6.237785"; PGA_scaffold66031__1_contigs__length_24994 StringTie transcript 1589 2290 1000 + . gene_id "STRG.21"; transcript_id "STRG.21.1"; reference_id "PGEN_00012761-RA"; ref_gene_id "PGEN_00012761"; cov "0.421652"; FPKM "2031.666185"; TPM "6277.833124"; PGA_scaffold66031__1_contigs__length_24994 StringTie exon 1589 2290 1000 + . gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; reference_id "PGEN_00012761-RA"; ref_gene_id "PGEN_00012761"; cov "0.421652"; PGA_scaffold68024__1_contigs__length_21067 StringTie transcript 14107 15427 1000 + . gene_id "STRG.22"; transcript_id "STRG.22.1"; cov "2.690583"; FPKM "12964.165943"; TPM "40059.174580"; PGA_scaffold68024__1_contigs__length_21067 StringTie exon 14107 14222 1000 + . gene_id "STRG.22"; transcript_id "STRG.22.1"; exon_number "1"; cov "2.741379"; PGA_scaffold68024__1_contigs__length_21067 StringTie exon 15321 15427 1000 + . gene_id "STRG.22"; transcript_id "STRG.22.1"; exon_number "2"; cov "2.635514"; PGA_scaffold235401__1_contigs__length_2101 StringTie transcript 279 1658 1000 - . gene_id "STRG.23"; transcript_id "STRG.23.1"; reference_id "PGEN_00044854-RA"; ref_gene_id "PGEN_00044854"; cov "0.218116"; FPKM "1050.958851"; TPM "3247.454891"; PGA_scaffold235401__1_contigs__length_2101 StringTie exon 279 1658 1000 - . gene_id "STRG.23"; transcript_id "STRG.23.1"; exon_number "1"; reference_id "PGEN_00044854-RA"; ref_gene_id "PGEN_00044854"; cov "0.218116";