Mercurial > repos > iuc > stringtie

comparison test-data/stringtie_merge_out2.gtf @ 6:d0bb240d7525 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
author iuc
date Wed, 13 Jul 2016 14:48:26 -0400
parents
children c84d44519b2e
comparison
equal deleted inserted replaced
5:f504b3b7e49d 6:d0bb240d7525
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
2 # StringTie version 1.2.3
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";
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";
7 chr1 StringTie transcript 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1";
8 chr1 StringTie exon 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1";
9 chr1 StringTie transcript 3204563 3661579 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; ref_gene_id "Xkr4";
10 chr1 StringTie exon 3204563 3207049 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "1"; ref_gene_id "Xkr4";
11 chr1 StringTie exon 3411783 3411982 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "2"; ref_gene_id "Xkr4";
12 chr1 StringTie exon 3660633 3661579 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "3"; ref_gene_id "Xkr4";
13 chr1 StringTie transcript 3212214 3212439 1000 . . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1";
14 chr1 StringTie exon 3212214 3212439 1000 . . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1";
15 chr1 StringTie transcript 3212718 3212801 1000 . . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1";
16 chr1 StringTie exon 3212718 3212801 1000 . . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1";
17 chr1 StringTie transcript 3213096 3213242 1000 . . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1";
18 chr1 StringTie exon 3213096 3213242 1000 . . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1";
19 chr1 StringTie transcript 3242634 3243079 1000 . . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1";
20 chr1 StringTie exon 3242634 3243079 1000 . . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1";
21 chr1 StringTie transcript 3243348 3243401 1000 . . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1";
22 chr1 StringTie exon 3243348 3243401 1000 . . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1";
23 chr1 StringTie transcript 3277914 3278390 1000 . . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1";
24 chr1 StringTie exon 3277914 3278390 1000 . . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; exon_number "1";
25 chr1 StringTie transcript 3280687 3280741 1000 . . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1";
26 chr1 StringTie exon 3280687 3280741 1000 . . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; exon_number "1";
27 chr1 StringTie transcript 3282761 3282832 1000 . . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1";
28 chr1 StringTie exon 3282761 3282832 1000 . . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; exon_number "1";
29 chr1 StringTie transcript 3290489 3291273 1000 . . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1";
30 chr1 StringTie exon 3290489 3291273 1000 . . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; exon_number "1";
31 chr1 StringTie transcript 3299444 3299664 1000 . . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1";
32 chr1 StringTie exon 3299444 3299664 1000 . . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; exon_number "1";
33 chr1 StringTie transcript 3319000 3319051 1000 . . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1";
34 chr1 StringTie exon 3319000 3319051 1000 . . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; exon_number "1";
35 chr1 StringTie transcript 3351241 3351311 1000 . . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1";
36 chr1 StringTie exon 3351241 3351311 1000 . . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "1";
37 chr1 StringTie transcript 3355908 3356119 1000 . . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1";
38 chr1 StringTie exon 3355908 3356119 1000 . . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "1";
39 chr1 StringTie transcript 3363077 3363446 1000 . . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1";
40 chr1 StringTie exon 3363077 3363446 1000 . . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "1";
41 chr1 StringTie transcript 3363754 3363849 1000 . . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1";
42 chr1 StringTie exon 3363754 3363849 1000 . . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "1";
43 chr1 StringTie transcript 3377212 3377262 1000 . . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1";
44 chr1 StringTie exon 3377212 3377262 1000 . . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; exon_number "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";
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";
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";
51 chr1 mm9_refFlat exon 4341991 4342162 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "2"; ref_gene_id "Rp1";
52 chr1 mm9_refFlat exon 4342283 4342918 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "3"; ref_gene_id "Rp1";
53 chr1 mm9_refFlat exon 4350281 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "4"; ref_gene_id "Rp1";
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";
56 chr1 mm9_refFlat exon 4483181 4483547 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "2"; ref_gene_id "Sox17";
57 chr1 mm9_refFlat exon 4483853 4483944 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "3"; ref_gene_id "Sox17";
58 chr1 mm9_refFlat exon 4485217 4486023 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "4"; ref_gene_id "Sox17";
59 chr1 mm9_refFlat exon 4486372 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "5"; ref_gene_id "Sox17";
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";
62 chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2"; ref_gene_id "Mrpl15";
63 chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3"; ref_gene_id "Mrpl15";
64 chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4"; ref_gene_id "Mrpl15";
65 chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5"; 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";
68 chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2"; ref_gene_id "Mrpl15";
69 chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3"; ref_gene_id "Mrpl15";
70 chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4"; ref_gene_id "Mrpl15";
71 chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5"; 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";
74 chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2"; ref_gene_id "Mrpl15";
75 chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3"; ref_gene_id "Mrpl15";
76 chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4"; ref_gene_id "Mrpl15";
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";
79 chr1 mm9_refFlat exon 4798536 4798567 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2"; ref_gene_id "Lypla1";
80 chr1 mm9_refFlat exon 4818665 4818730 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3"; ref_gene_id "Lypla1";
81 chr1 mm9_refFlat exon 4820349 4820396 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4"; ref_gene_id "Lypla1";
82 chr1 mm9_refFlat exon 4822392 4822462 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5"; ref_gene_id "Lypla1";
83 chr1 mm9_refFlat exon 4827082 4827155 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6"; ref_gene_id "Lypla1";
84 chr1 mm9_refFlat exon 4829468 4829569 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7"; ref_gene_id "Lypla1";
85 chr1 mm9_refFlat exon 4831037 4831213 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8"; ref_gene_id "Lypla1";
86 chr1 mm9_refFlat exon 4835044 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9"; ref_gene_id "Lypla1";
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";
89 chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2"; 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";
92 chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2"; ref_gene_id "Tcea1";
93 chr1 mm9_refFlat exon 4868108 4868213 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3"; ref_gene_id "Tcea1";
94 chr1 mm9_refFlat exon 4876825 4876912 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4"; ref_gene_id "Tcea1";
95 chr1 mm9_refFlat exon 4879538 4879683 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5"; ref_gene_id "Tcea1";
96 chr1 mm9_refFlat exon 4880821 4880877 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6"; ref_gene_id "Tcea1";
97 chr1 mm9_refFlat exon 4881996 4882150 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7"; ref_gene_id "Tcea1";
98 chr1 mm9_refFlat exon 4883498 4883644 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8"; ref_gene_id "Tcea1";
99 chr1 mm9_refFlat exon 4885015 4885086 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9"; ref_gene_id "Tcea1";
100 chr1 mm9_refFlat exon 4886437 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10"; ref_gene_id "Tcea1";