how to download gene annotation bed file from ensembl?
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8.8 years ago
Ati ▴ 50

Sorry it maybe really a naive question but I want to know how I could download gene annotation bed file from Ensembl?

ensembl RNA-Seq genome ucsc • 12k views
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Entering edit mode
8.8 years ago
Amitm ★ 2.3k

hi,

I am not sure if you can get it in BED format per se, but you could -

  1. Anno file in GTF format from here

    I am assuming you are looking for human. If not, go in here and choose your organism - ftp://ftp.ensembl.org/pub/release-83/gtf/

  2. And of course you can use BioMart -

    Here too choose your organism.

Once you have used either of the above, you can shuffle the columns of the final file to make a BED i.e.

chr<TAB>Strt<TAB>End

in its simplest form.

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