Question: Chip-Seq : how to test if several genomic regions are enriched in histone marks
gravatar for Nicolas Rosewick
5.5 years ago by
Belgium, Brussels
Nicolas Rosewick8.6k wrote:


Simple question but I'm a little bit new in the epigenetic world. So I've a bunch of very small region (~100b) and I want to know if these regions are enriched in histone marks. 

My idea was to use ENCODE data and to intersect them with my input regions, to compute a score and to perform like a randomization test by picking random small region, and comparing random score with my input score. But do I have to use the signal bigwig file ( bigWigAverageOverBed can compute the average score for a region from a bigwig file )? or the peak file ? 

Other ideas ?


ADD COMMENTlink modified 5.5 years ago by dariober10k • written 5.5 years ago by Nicolas Rosewick8.6k
gravatar for dariober
5.5 years ago by
WCIP | Glasgow | UK
dariober10k wrote:

Have a look at Genometricorr and GAT packages, they might point you in the right direction.

ADD COMMENTlink modified 7 months ago by RamRS25k • written 5.5 years ago by dariober10k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1619 users visited in the last hour