Mercurial > repos > iuc > stringtie

comparison test-data/stringtie_merge_out2.gtf @ 10:c84d44519b2e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
author iuc
date Tue, 04 Apr 2017 12:58:27 -0400
parents d0bb240d7525
children dd4df992d93d
comparison
equal deleted inserted replaced
9:1f23fc7df25c 10:c84d44519b2e
1 # 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 1 # stringtie --merge -p 1 -G /tmp/tmpJfKWNy/files/000/dataset_46.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpJfKWNy/files/000/dataset_47.dat /tmp/tmpJfKWNy/files/000/dataset_44.dat /tmp/tmpJfKWNy/files/000/dataset_45.dat
2 # StringTie version 1.2.3 2 # StringTie version 1.3.3
3 chr1 StringTie transcript 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; 3 chr1 StringTie transcript 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1";
4 chr1 StringTie exon 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; 4 chr1 StringTie exon 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1";
5 chr1 StringTie transcript 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; 5 chr1 StringTie transcript 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1";
6 chr1 StringTie exon 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; 6 chr1 StringTie exon 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1";
7 chr1 StringTie transcript 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; 7 chr1 StringTie transcript 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1";
45 chr1 StringTie transcript 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; 45 chr1 StringTie transcript 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1";
46 chr1 StringTie exon 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; exon_number "1"; 46 chr1 StringTie exon 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; exon_number "1";
47 chr1 StringTie transcript 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; 47 chr1 StringTie transcript 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1";
48 chr1 StringTie exon 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1"; 48 chr1 StringTie exon 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1";
49 chr1 mm9_refFlat transcript 4334224 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1"; 49 chr1 mm9_refFlat transcript 4334224 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1";
50 chr1 mm9_refFlat exon 4334224 4340172 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "1"; ref_gene_id "Rp1"; 50 chr1 mm9_refFlat exon 4334224 4340172 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "1";
51 chr1 mm9_refFlat exon 4341991 4342162 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "2"; ref_gene_id "Rp1"; 51 chr1 mm9_refFlat exon 4341991 4342162 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "2";
52 chr1 mm9_refFlat exon 4342283 4342918 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "3"; ref_gene_id "Rp1"; 52 chr1 mm9_refFlat exon 4342283 4342918 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "3";
53 chr1 mm9_refFlat exon 4350281 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "4"; ref_gene_id "Rp1"; 53 chr1 mm9_refFlat exon 4350281 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "4";
54 chr1 mm9_refFlat transcript 4481009 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17"; 54 chr1 mm9_refFlat transcript 4481009 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17";
55 chr1 mm9_refFlat exon 4481009 4482749 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "1"; ref_gene_id "Sox17"; 55 chr1 mm9_refFlat exon 4481009 4482749 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "1";
56 chr1 mm9_refFlat exon 4483181 4483547 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "2"; ref_gene_id "Sox17"; 56 chr1 mm9_refFlat exon 4483181 4483547 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "2";
57 chr1 mm9_refFlat exon 4483853 4483944 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "3"; ref_gene_id "Sox17"; 57 chr1 mm9_refFlat exon 4483853 4483944 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "3";
58 chr1 mm9_refFlat exon 4485217 4486023 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "4"; ref_gene_id "Sox17"; 58 chr1 mm9_refFlat exon 4485217 4486023 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "4";
59 chr1 mm9_refFlat exon 4486372 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "5"; ref_gene_id "Sox17"; 59 chr1 mm9_refFlat exon 4486372 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "5";
60 chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15"; 60 chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15";
61 chr1 mm9_refFlat exon 4763279 4766882 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1"; ref_gene_id "Mrpl15"; 61 chr1 mm9_refFlat exon 4763279 4766882 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1";
62 chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2"; ref_gene_id "Mrpl15"; 62 chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2";
63 chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3"; ref_gene_id "Mrpl15"; 63 chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3";
64 chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4"; ref_gene_id "Mrpl15"; 64 chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4";
65 chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5"; ref_gene_id "Mrpl15"; 65 chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5";
66 chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15"; 66 chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15";
67 chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1"; ref_gene_id "Mrpl15"; 67 chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1";
68 chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2"; ref_gene_id "Mrpl15"; 68 chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2";
69 chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3"; ref_gene_id "Mrpl15"; 69 chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3";
70 chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4"; ref_gene_id "Mrpl15"; 70 chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4";
71 chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5"; ref_gene_id "Mrpl15"; 71 chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5";
72 chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15"; 72 chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15";
73 chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1"; ref_gene_id "Mrpl15"; 73 chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1";
74 chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2"; ref_gene_id "Mrpl15"; 74 chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2";
75 chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3"; ref_gene_id "Mrpl15"; 75 chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3";
76 chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4"; ref_gene_id "Mrpl15"; 76 chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4";
77 chr1 mm9_refFlat transcript 4797974 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1"; 77 chr1 mm9_refFlat transcript 4797974 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1";
78 chr1 mm9_refFlat exon 4797974 4798063 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1"; ref_gene_id "Lypla1"; 78 chr1 mm9_refFlat exon 4797974 4798063 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1";
79 chr1 mm9_refFlat exon 4798536 4798567 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2"; ref_gene_id "Lypla1"; 79 chr1 mm9_refFlat exon 4798536 4798567 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2";
80 chr1 mm9_refFlat exon 4818665 4818730 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3"; ref_gene_id "Lypla1"; 80 chr1 mm9_refFlat exon 4818665 4818730 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3";
81 chr1 mm9_refFlat exon 4820349 4820396 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4"; ref_gene_id "Lypla1"; 81 chr1 mm9_refFlat exon 4820349 4820396 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4";
82 chr1 mm9_refFlat exon 4822392 4822462 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5"; ref_gene_id "Lypla1"; 82 chr1 mm9_refFlat exon 4822392 4822462 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5";
83 chr1 mm9_refFlat exon 4827082 4827155 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6"; ref_gene_id "Lypla1"; 83 chr1 mm9_refFlat exon 4827082 4827155 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6";
84 chr1 mm9_refFlat exon 4829468 4829569 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7"; ref_gene_id "Lypla1"; 84 chr1 mm9_refFlat exon 4829468 4829569 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7";
85 chr1 mm9_refFlat exon 4831037 4831213 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8"; ref_gene_id "Lypla1"; 85 chr1 mm9_refFlat exon 4831037 4831213 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8";
86 chr1 mm9_refFlat exon 4835044 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9"; ref_gene_id "Lypla1"; 86 chr1 mm9_refFlat exon 4835044 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9";
87 chr1 mm9_refFlat transcript 4847775 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1"; 87 chr1 mm9_refFlat transcript 4847775 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";
88 chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1"; ref_gene_id "Tcea1"; 88 chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1";
89 chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2"; ref_gene_id "Tcea1"; 89 chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2";
90 chr1 mm9_refFlat transcript 4847775 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1"; 90 chr1 mm9_refFlat transcript 4847775 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";
91 chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1"; ref_gene_id "Tcea1"; 91 chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1";
92 chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2"; ref_gene_id "Tcea1"; 92 chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2";
93 chr1 mm9_refFlat exon 4868108 4868213 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3"; ref_gene_id "Tcea1"; 93 chr1 mm9_refFlat exon 4868108 4868213 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3";
94 chr1 mm9_refFlat exon 4876825 4876912 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4"; ref_gene_id "Tcea1"; 94 chr1 mm9_refFlat exon 4876825 4876912 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4";
95 chr1 mm9_refFlat exon 4879538 4879683 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5"; ref_gene_id "Tcea1"; 95 chr1 mm9_refFlat exon 4879538 4879683 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5";
96 chr1 mm9_refFlat exon 4880821 4880877 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6"; ref_gene_id "Tcea1"; 96 chr1 mm9_refFlat exon 4880821 4880877 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6";
97 chr1 mm9_refFlat exon 4881996 4882150 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7"; ref_gene_id "Tcea1"; 97 chr1 mm9_refFlat exon 4881996 4882150 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7";
98 chr1 mm9_refFlat exon 4883498 4883644 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8"; ref_gene_id "Tcea1"; 98 chr1 mm9_refFlat exon 4883498 4883644 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8";
99 chr1 mm9_refFlat exon 4885015 4885086 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9"; ref_gene_id "Tcea1"; 99 chr1 mm9_refFlat exon 4885015 4885086 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9";
100 chr1 mm9_refFlat exon 4886437 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10"; ref_gene_id "Tcea1"; 100 chr1 mm9_refFlat exon 4886437 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10";