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 ?