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

ADD COMMENTlink 4.0 years ago abc • 30 • updated 4.0 years ago shivani967452 • 0
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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 - http://www.ensembl.org/info/data/ftp/index.html

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. chrStrtEnd

in its simplest form.

ADD COMMENTlink 4.0 years ago Amitm ♦ 1.6k

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