Is There A Way To Download The Human Exome?

Question

[Jordan]

Hi,

Is there a way to get human exome? I will need it for one of my analysis. It is alright if it is bed format or fasta.

Thanks!

[Pierre Lindenbaum]

"exome sequence"/BED or FASTA ? Please Clarify .

[Jordan]

Both BED and FASTA are fine. Editing sequence part.

Answer 1

[Pierre Lindenbaum]

get the exons as BED:

Exon coordinates of hg19 genome download

extract the FASTA sequences using bedtools getfasta: http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html

[Jordan]

Thanks for the link Pierre. I downloaded this file and I found the length of the exome (sum of all exon lengths) to be 216,018,204 bp. Does it sound right?

[Pierre Lindenbaum]

exons overlap. The size of the human exome is ~50M. Use bedtools 'mergeBed' to merge all those exons.