Question: Chip-Seq : how to test if several genomic regions are enriched in histone marks
gravatar for Nicolas Rosewick
6.4 years ago by
Belgium, Brussels
Nicolas Rosewick9.2k 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 6.4 years ago by dariober11k • written 6.4 years ago by Nicolas Rosewick9.2k
gravatar for dariober
6.4 years ago by
WCIP | Glasgow | UK
dariober11k wrote:

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

ADD COMMENTlink modified 17 months ago by _r_am31k • written 6.4 years ago by dariober11k
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