I have ChIP-seq data of stalled Pol2 (13.000 peaks) and a protein that mostly binds in promoter regions (250 peaks). Now I want to know whether there is a significant overlap between the two.
What I did try so far, is using "bedtools fisher" with the two datasets. However, as far as I understand, this will not take care of the fact, that both datasets mostly bind in promoter regions. Of course, it's telling me that the overlap is extremely significant.
In other words: I want to know whether my protein of interest binds significantly more often than expected to a region where Pol2 is sitting, considering that Pol2 already occupies a large fraction of promoters with its 13.000 peaks.
Any ideas on how to do this properly?