Convert fasta to bed (no gtf available)

Question

[bioinfo8]

Hi,

I have a genome for which only fasta file is available for CDS from Ensembl and no gtf. But I need bed file of its CDS. Any guidance would be appreciated!

Thanks.

[Emily]

What genome is that? We should have a GTF for everything.

[bioinfo8]

Emily, I emailed you the link.

[Emily]

I haven't received this. Can you just tell me what species it is, please? Here.

[bioinfo8]

May be I can try samtools and awk (Gff Or Bed File For Hg19 Genome )

[WouterDeCoster]

Not nice to delete a thread after you received helpful answers.

[bioinfo8]

Sorry, it was just by mistake, wanted to close post (not to annoy more people) but hit on delete. :P

[WouterDeCoster]

I moved a comment to an answer so you can accept it to mark this thread as resolved.

Answer 1

[Emily]

I got your email. You were looking at zebrafish release 79. I'm not sure why you couldn't just write it here and instead had to sneak around trying to find my email address to send to me directly.

The GTF is here: ftp://ftp.ensembl.org/pub/release-79/gtf/danio_rerio/

[bioinfo8]

I tried to paste the link, but did not appear, don't know why :P