Some software requires bed12 format, not gtf/gff. So a convertion work should be done.
bedops gtf2bed
Easy way to get your result —- bedops
gtf2bed < Homo_sapiens.GRCh38.85.gtf | head 1 11868 14409 ENST00000456328 0 + 11868 14409 0 3 359,109,1189, 0,744,1352, 1 12009 13670 ENST00000450305 0 + 12009 13670 0 6 48,49,85,78,154,218, 0,169,603,965,1211,1443, 1 17368 17436 ENST00000619216 0 - 17368 17436 0 1 68, 0, 1 14403 29570 ENST00000488147 0 - 14403 29570 0 11 98,34,152,159,198,136,137,147,99,154,37, 0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130, 1 29553 31097 ENST00000473358 0 + 29553 31097 0 3 486,104,122, 0,1010,1422, 1 30266 31109 ENST00000469289 0 + 30266 31109 0 2 401,134, 0,709, 1 30365 30503 ENST00000607096 0 + 30365 30503 0 1 138, 0, 1 34553 36081 ENST00000417324 0 - 34553 36081 0 3 621,205,361, 0,723,1167, 1 35244 36073 ENST00000461467 0 - 35244 36073 0 2 237,353, 0,476, 1 52472 53312 ENST00000606857 0 + 52472 53312 0 1 840, 0,
Here we use UCSC’s package to convert gtf format file to bed12 format file.
Download UCSC package
wget -c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred wget -c http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToBed chmod 755 gtfToGenePred genePredToBed
Convert gtf to bed12
time gtfToGenePred Homo_sapiens.GRCh38.85.gtf test.genePhred && genePredToBed test.genePhred result.bed && rm test.genePhred real 0m14.959s user 0m14.387s sys 0m0.567s
head reult.bed 1 11868 14409 ENST00000456328 0 + 14409 14409 0 3 359,109,1189, 0,744,1352, 1 12009 13670 ENST00000450305 0 + 13670 13670 0 6 48,49,85,78,154,218, 0,169,603,965,1211,1443, 1 14403 29570 ENST00000488147 0 - 29570 29570 0 11 98,34,152,159,198,136,137,147,99,154,37, 0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130, 1 17368 17436 ENST00000619216 0 - 17436 17436 0 1 68, 0, 1 29553 31097 ENST00000473358 0 + 31097 31097 0 3 486,104,122, 0,1010,1422, 1 30266 31109 ENST00000469289 0 + 31109 31109 0 2 401,134, 0,709, 1 30365 30503 ENST00000607096 0 + 30503 30503 0 1 138, 0, 1 34553 36081 ENST00000417324 0 - 36081 36081 0 3 621,205,361, 0,723,1167, 1 35244 36073 ENST00000461467 0 - 36073 36073 0 2 237,353, 0,476, 1 52472 53312 ENST00000606857 0 + 53312 53312 0 1 840, 0,
Cheers.
Another tool
I also recommend a perl script — gtf2bed. This script works fine to convert gtf to bed format. Thanks for ea-utils project.
Ref
https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/fTNuZOS-CYA
https://expressionanalysis.github.io/ea-utils/
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