gff to bed12 conversion with proper exon columns

Question

[goldberry88]

Hi all,

I'm bashing my head against a wall here..

I need something to convert a gff to a bed file with 12 columns, that properly displays exons for annotation purposes. I've found and tried many, many conversion tools that convert from gff to bed, but in the gff the exons are listed as separate lines (is this normal?) and as such whichever tool I use seems to give me a bed file where exons are listed as separate lines as well, where I need them to be part of the 'transcript' line in the bed file.

Is there any way to do this without writing a tool from scratch for this?

Thank you in advance!

Answer 1

[Juke34]

What tools did you use?

in gff the exons are listed as separate lines (is this normal?)

Yes it is

See here for a list of conversion tools https://agat.readthedocs.io/en/latest/gff_to_bed.html Among the 4 only bedops here gives a bed line for each gff exon feature/line.

[goldberry88]

Ah,

I've tried bed-tools, and some old ones that don't seem to be maintained anymore, and tend to be a bit buggy..

But thank you very much, this link is very usefull! I haven't heard from these tools before!