diff test-data/cuffmerge_out1.gtf @ 0:dbbd37e013aa

Uploaded tool tarball.
author devteam
date Tue, 01 Oct 2013 12:57:24 -0400
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffmerge_out1.gtf	Tue Oct 01 12:57:24 2013 -0400
@@ -0,0 +1,74 @@
+chr1	Cufflinks	exon	4797974	4798063	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4798536	4798567	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4818665	4818730	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4820349	4820396	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4822392	4822462	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "5"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4827082	4827155	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "6"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4829468	4829569	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "7"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4831037	4831213	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "8"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4835044	4836816	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "9"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4847775	4848057	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4857551	4857613	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4847775	4848057	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4857551	4857613	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4868108	4868213	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "3"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4876825	4876912	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "4"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4879538	4879683	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "5"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4880821	4880877	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "6"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4881996	4882150	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "7"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4883498	4883644	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "8"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4885015	4885086	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "9"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4886437	4887987	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "10"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	3204563	3207049	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "1"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
+chr1	Cufflinks	exon	3411783	3411982	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "2"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
+chr1	Cufflinks	exon	3660633	3661579	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "3"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
+chr1	Cufflinks	exon	4334224	4340172	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "1"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4341991	4342162	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "2"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4342283	4342918	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "3"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4350281	4350473	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "4"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4481009	4482749	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "1"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4483181	4483547	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "2"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4483853	4483944	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "3"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4485217	4486023	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "4"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4486372	4486494	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "5"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4763279	4764597	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4763279	4764597	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4774032	4774186	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4763279	4766882	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4774032	4774186	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	3111450	3111490	.	.	.	gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS7";
+chr1	Cufflinks	exon	3111546	3111576	.	.	.	gene_id "XLOC_000008"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.2.1"; class_code "u"; tss_id "TSS8";
+chr1	Cufflinks	exon	3174766	3174792	.	.	.	gene_id "XLOC_000009"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS9";
+chr1	Cufflinks	exon	3187402	3187428	.	.	.	gene_id "XLOC_000010"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.4.1"; class_code "u"; tss_id "TSS10";
+chr1	Cufflinks	exon	3188522	3188548	.	.	.	gene_id "XLOC_000011"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS11";
+chr1	Cufflinks	exon	3189811	3190789	.	.	.	gene_id "XLOC_000012"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.6.1"; class_code "u"; tss_id "TSS12";
+chr1	Cufflinks	exon	3190859	3191434	.	.	.	gene_id "XLOC_000013"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS13";
+chr1	Cufflinks	exon	3191513	3192077	.	.	.	gene_id "XLOC_000014"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.8.1"; class_code "u"; tss_id "TSS14";
+chr1	Cufflinks	exon	3192251	3192336	.	.	.	gene_id "XLOC_000015"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS15";
+chr1	Cufflinks	exon	3192442	3192494	.	.	.	gene_id "XLOC_000016"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.10.1"; class_code "u"; tss_id "TSS16";
+chr1	Cufflinks	exon	3192551	3192676	.	.	.	gene_id "XLOC_000017"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS17";
+chr1	Cufflinks	exon	3192732	3192811	.	.	.	gene_id "XLOC_000018"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.12.1"; class_code "u"; tss_id "TSS18";
+chr1	Cufflinks	exon	3192941	3193042	.	.	.	gene_id "XLOC_000019"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS19";
+chr1	Cufflinks	exon	3194186	3194226	.	.	.	gene_id "XLOC_000020"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.14.1"; class_code "u"; tss_id "TSS20";
+chr1	Cufflinks	exon	3194303	3194329	.	.	.	gene_id "XLOC_000021"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS21";
+chr1	Cufflinks	exon	3194707	3194733	.	.	.	gene_id "XLOC_000022"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.16.1"; class_code "u"; tss_id "TSS22";
+chr1	Cufflinks	exon	3195084	3195110	.	.	.	gene_id "XLOC_000023"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS23";
+chr1	Cufflinks	exon	3195451	3195477	.	.	.	gene_id "XLOC_000024"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.18.1"; class_code "u"; tss_id "TSS24";
+chr1	Cufflinks	exon	3197090	3197116	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS25";
+chr1	Cufflinks	exon	3197247	3197273	.	.	.	gene_id "XLOC_000026"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.20.1"; class_code "u"; tss_id "TSS26";
+chr1	Cufflinks	exon	3197347	3197373	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS27";
+chr1	Cufflinks	exon	3197426	3197452	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.22.1"; class_code "u"; tss_id "TSS28";
+chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000032"; exon_number "1"; oId "CUFF.23.1"; class_code "u"; tss_id "TSS29";
+chr1	Cufflinks	exon	3200326	3200352	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.24.1"; class_code "u"; tss_id "TSS30";
+chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000031"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; tss_id "TSS31";
+chr1	Cufflinks	exon	3201008	3201481	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000035"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS32";
+chr1	Cufflinks	exon	3201597	3201809	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000036"; exon_number "1"; oId "CUFF.27.1"; class_code "u"; tss_id "TSS33";