gtf2bed wrong output.

[GoogleCodeExporter]

Hi,

I have been using using the gt2bed perl script for conversion. Recently I came 
across this. 

I downloaded gtf file (refflat hg19) from ucsc table browser. When I convert 
this gtf to bed, I see some of the transcripts have wrong info. 

For. eg: gtf file has 2 entries for transcript 'LOC100133331', one on 
chromsome-1 (4 exons) and chromosome-5 (4 exons). But the script produces 
single entry for both the transcripts, as a transcript on chromsome-1 with 8 
exons. I guess chr5 entry was concatenated with the chr1 entry since tx id was 
same. 

Also bed file produced by the script has lot lesser transcripts than in gtf 
file.

Original issue reported on code.google.com by anand...@gmail.com on 30 Oct 2014 at 10:11

[GoogleCodeExporter]

can you attach the gtf?

Original comment by earone...@gmail.com on 16 Dec 2014 at 9:27