how to download gene annotation bed file from ensembl?

Question

[Ati]

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

Answer 1

[Amitm]

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.