Mercurial > repos > iuc > stringtie
diff test-data/stringtie_merge_out2.gtf @ 20:cef79931dda5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb
| author | iuc |
|---|---|
| date | Wed, 27 Jul 2022 09:28:15 +0000 |
| parents | 258d696dbd7e |
| children | 914cfcba0ec8 |
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--- a/test-data/stringtie_merge_out2.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_merge_out2.gtf Wed Jul 27 09:28:15 2022 +0000 @@ -1,100 +1,100 @@ -# stringtie --merge -p 1 -G /tmp/tmp9cgbzsli/files/d/3/d/dataset_d3debef6-0cc0-44aa-898c-086d4fa8adb0.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmp9cgbzsli/files/b/4/d/dataset_b4dd908f-5f52-428f-bc2c-ba62cd00a83e.dat /tmp/tmp9cgbzsli/files/8/1/a/dataset_81a6719e-2f36-40ca-9d63-325d6eadd1d3.dat /tmp/tmp9cgbzsli/files/2/2/f/dataset_22f857ec-0df8-40d8-ba00-28b709b98b03.dat -# StringTie version 2.1.7 -chr1 StringTie transcript 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; -chr1 StringTie exon 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; -chr1 StringTie transcript 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; -chr1 StringTie exon 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; -chr1 StringTie transcript 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; -chr1 StringTie exon 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; -chr1 StringTie transcript 3204563 3661579 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; -chr1 StringTie exon 3204563 3207049 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "1"; ref_gene_id "Xkr4"; -chr1 StringTie exon 3411783 3411982 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "2"; ref_gene_id "Xkr4"; -chr1 StringTie exon 3660633 3661579 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "3"; ref_gene_id "Xkr4"; -chr1 StringTie transcript 3212214 3212439 1000 . . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; -chr1 StringTie exon 3212214 3212439 1000 . . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; -chr1 StringTie transcript 3212718 3212801 1000 . . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; -chr1 StringTie exon 3212718 3212801 1000 . . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; -chr1 StringTie transcript 3213096 3213242 1000 . . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; -chr1 StringTie exon 3213096 3213242 1000 . . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; -chr1 StringTie transcript 3242634 3243079 1000 . . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; -chr1 StringTie exon 3242634 3243079 1000 . . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; -chr1 StringTie transcript 3243348 3243401 1000 . . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; -chr1 StringTie exon 3243348 3243401 1000 . . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; -chr1 StringTie transcript 3277914 3278390 1000 . . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; -chr1 StringTie exon 3277914 3278390 1000 . . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; exon_number "1"; -chr1 StringTie transcript 3280687 3280741 1000 . . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; -chr1 StringTie exon 3280687 3280741 1000 . . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; exon_number "1"; -chr1 StringTie transcript 3282761 3282832 1000 . . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; -chr1 StringTie exon 3282761 3282832 1000 . . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; exon_number "1"; -chr1 StringTie transcript 3290489 3291273 1000 . . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; -chr1 StringTie exon 3290489 3291273 1000 . . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; exon_number "1"; -chr1 StringTie transcript 3299444 3299664 1000 . . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; -chr1 StringTie exon 3299444 3299664 1000 . . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; exon_number "1"; -chr1 StringTie transcript 3319000 3319051 1000 . . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; -chr1 StringTie exon 3319000 3319051 1000 . . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; exon_number "1"; -chr1 StringTie transcript 3351241 3351311 1000 . . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; -chr1 StringTie exon 3351241 3351311 1000 . . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "1"; -chr1 StringTie transcript 3355908 3356119 1000 . . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; -chr1 StringTie exon 3355908 3356119 1000 . . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "1"; -chr1 StringTie transcript 3363077 3363446 1000 . . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; -chr1 StringTie exon 3363077 3363446 1000 . . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "1"; -chr1 StringTie transcript 3363754 3363849 1000 . . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; -chr1 StringTie exon 3363754 3363849 1000 . . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "1"; -chr1 StringTie transcript 3377212 3377262 1000 . . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; -chr1 StringTie exon 3377212 3377262 1000 . . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; exon_number "1"; -chr1 StringTie transcript 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; -chr1 StringTie exon 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; exon_number "1"; -chr1 StringTie transcript 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; -chr1 StringTie exon 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1"; -chr1 mm9_refFlat transcript 4334224 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1"; -chr1 mm9_refFlat exon 4334224 4340172 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "1"; -chr1 mm9_refFlat exon 4341991 4342162 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "2"; -chr1 mm9_refFlat exon 4342283 4342918 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "3"; -chr1 mm9_refFlat exon 4350281 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "4"; -chr1 mm9_refFlat transcript 4481009 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17"; -chr1 mm9_refFlat exon 4481009 4482749 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "1"; -chr1 mm9_refFlat exon 4483181 4483547 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "2"; -chr1 mm9_refFlat exon 4483853 4483944 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "3"; -chr1 mm9_refFlat exon 4485217 4486023 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "4"; -chr1 mm9_refFlat exon 4486372 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "5"; -chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15"; -chr1 mm9_refFlat exon 4763279 4766882 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1"; -chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2"; -chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3"; -chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4"; -chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5"; -chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15"; -chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1"; -chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2"; -chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3"; -chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4"; -chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5"; -chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15"; -chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1"; -chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2"; -chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3"; -chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4"; -chr1 mm9_refFlat transcript 4797974 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1"; -chr1 mm9_refFlat exon 4797974 4798063 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1"; -chr1 mm9_refFlat exon 4798536 4798567 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2"; -chr1 mm9_refFlat exon 4818665 4818730 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3"; -chr1 mm9_refFlat exon 4820349 4820396 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4"; -chr1 mm9_refFlat exon 4822392 4822462 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5"; -chr1 mm9_refFlat exon 4827082 4827155 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6"; -chr1 mm9_refFlat exon 4829468 4829569 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7"; -chr1 mm9_refFlat exon 4831037 4831213 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8"; -chr1 mm9_refFlat exon 4835044 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9"; -chr1 mm9_refFlat transcript 4847775 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1"; -chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1"; -chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2"; -chr1 mm9_refFlat transcript 4847775 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1"; -chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1"; -chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2"; -chr1 mm9_refFlat exon 4868108 4868213 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3"; -chr1 mm9_refFlat exon 4876825 4876912 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4"; -chr1 mm9_refFlat exon 4879538 4879683 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5"; -chr1 mm9_refFlat exon 4880821 4880877 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6"; -chr1 mm9_refFlat exon 4881996 4882150 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7"; -chr1 mm9_refFlat exon 4883498 4883644 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8"; -chr1 mm9_refFlat exon 4885015 4885086 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9"; -chr1 mm9_refFlat exon 4886437 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10"; +# StringTie version 2\.1\.7 +# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat +chr1\tStringTie\texon\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3204563\t3207049\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; +chr1\tStringTie\texon\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3411783\t3411982\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; +chr1\tStringTie\texon\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; +chr1\tStringTie\texon\t3660633\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; +chr1\tStringTie\ttranscript\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3204563\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; +chr1\tStringTie\ttranscript\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tStringTie\ttranscript\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; +chr1\tmm9_refFlat\texon\t4334224\t4340172\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+"; +chr1\tmm9_refFlat\texon\t4341991\t4342162\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+"; +chr1\tmm9_refFlat\texon\t4342283\t4342918\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+"; +chr1\tmm9_refFlat\texon\t4350281\t4350473\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+"; +chr1\tmm9_refFlat\texon\t4481009\t4482749\t\.\t-\t\.\tgene_id "Sox17"; 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