Chip-Seq : how to test if several genomic regions are enriched in histone marks

Question

[Nicolas Rosewick]

Hi,

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?

Thanks

Answer 1

[dariober]

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