Question

Convert fasta to bed (no gtf available)

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8.5 years ago

bioinfo8 ▴ 230

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.

genome ensembl bed fasta CDS • 3.5k views

ADD COMMENT • link 8.5 years ago by bioinfo8 ▴ 230

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

ADD REPLY • link 8.5 years ago by Emily 24k

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Emily, I emailed you the link.

ADD REPLY • link 8.5 years ago by bioinfo8 ▴ 230

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

ADD REPLY • link 8.5 years ago by Emily 24k

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

ADD REPLY • link 8.5 years ago by bioinfo8 ▴ 230

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

ADD REPLY • link 8.5 years ago by WouterDeCoster 48k

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

ADD REPLY • link 8.5 years ago by bioinfo8 ▴ 230

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

ADD REPLY • link 8.5 years ago by WouterDeCoster 48k

score 5 · Accepted Answer · 2017-04-27

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8.5 years ago

Emily 24k

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/

ADD COMMENT • link 8.5 years ago by Emily 24k

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

ADD REPLY • link 8.5 years ago by bioinfo8 ▴ 230