Entering edit mode
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?
Sorry it maybe really a naive question but I want to know how I could download gene annotation bed file from Ensembl?
hi,
I am not sure if you can get it in BED format per se, but you could -
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/
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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