view test-data/stringtie_merge_out2.gtf @ 8:3437d5a5041c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46d41c5fec10407bd6b5cb77a11d9b43b82b95e
author iuc
date Fri, 23 Sep 2016 12:18:11 -0400
parents d0bb240d7525
children c84d44519b2e
line wrap: on
line source

# stringtie --merge -p 1 -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_9.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_10.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_7.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_8.dat
# StringTie version 1.2.3
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"; ref_gene_id "Rp1";
chr1	mm9_refFlat	exon	4341991	4342162	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "2"; ref_gene_id "Rp1";
chr1	mm9_refFlat	exon	4342283	4342918	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "3"; ref_gene_id "Rp1";
chr1	mm9_refFlat	exon	4350281	4350473	.	-	.	gene_id "Rp1"; transcript_id "Rp1"; exon_number "4"; ref_gene_id "Rp1";
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"; ref_gene_id "Sox17";
chr1	mm9_refFlat	exon	4483181	4483547	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "2"; ref_gene_id "Sox17";
chr1	mm9_refFlat	exon	4483853	4483944	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "3"; ref_gene_id "Sox17";
chr1	mm9_refFlat	exon	4485217	4486023	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "4"; ref_gene_id "Sox17";
chr1	mm9_refFlat	exon	4486372	4486494	.	-	.	gene_id "Sox17"; transcript_id "Sox17"; exon_number "5"; ref_gene_id "Sox17";
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"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5"; ref_gene_id "Mrpl15";
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"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4774032	4774186	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5"; ref_gene_id "Mrpl15";
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"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4767606	4767729	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4772649	4772814	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3"; ref_gene_id "Mrpl15";
chr1	mm9_refFlat	exon	4775654	4775807	.	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4"; ref_gene_id "Mrpl15";
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"; ref_gene_id "Lypla1";
chr1	mm9_refFlat	exon	4798536	4798567	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2"; ref_gene_id "Lypla1";
chr1	mm9_refFlat	exon	4818665	4818730	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3"; ref_gene_id "Lypla1";
chr1	mm9_refFlat	exon	4820349	4820396	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4"; ref_gene_id "Lypla1";
chr1	mm9_refFlat	exon	4822392	4822462	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5"; ref_gene_id "Lypla1";
chr1	mm9_refFlat	exon	4827082	4827155	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6"; ref_gene_id "Lypla1";
chr1	mm9_refFlat	exon	4829468	4829569	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7"; ref_gene_id "Lypla1";
chr1	mm9_refFlat	exon	4831037	4831213	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8"; ref_gene_id "Lypla1";
chr1	mm9_refFlat	exon	4835044	4836816	.	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9"; ref_gene_id "Lypla1";
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"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2"; ref_gene_id "Tcea1";
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"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4857551	4857613	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4868108	4868213	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4876825	4876912	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4879538	4879683	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4880821	4880877	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4881996	4882150	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4883498	4883644	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4885015	4885086	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9"; ref_gene_id "Tcea1";
chr1	mm9_refFlat	exon	4886437	4887987	.	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10"; ref_gene_id "Tcea1";