I have a list of enhancers elements that I care about (about 70,000 in number, each exactly 3000 bp long in terms of genomic location). I also have total RNA-seq reads from an experiment (3 replicates, mouse), which I have mapped and gathered counts for these enhancer elements using featurecounts. Now, I want to know which of these enhancers have some meaningful expression level. For this, my plan is to get the basal expected expression level, and then if the expression level for an enhancer is greater than this, I would call it as being truly expressed. I have heard that Poisson distribution can be a good tool for such count-based modeling, but I am not sure how to go about it. Could anyone provide any help/ideas?
PS - I am completely OK with an approximate method for now, I am not trying to be too precise since it is a preliminary identification of expressed enhancers.
Thank you in advance!