My first time posting on Biostars. We are analyzing the distribution of RNA polymerase across a Eukaryotic genome. The distribution, as you might imagine, is broad, spanning entire genes and beyond. We have used MACS2 "corrected" for broad peaks, but the results are highly unsatisfactory. There are genes for which I can clearly see by eye that RNAPII accumulation is well above background and yet MACS2 does not call a peak. Now, keeping in mind that I know next to nothing about bioinformatics, why can I not simply employ a program (create one if it doesn't exist) to simply calculate the area under the curve, say between the start and stop codons, of every gene, for both experimental and input, and use the difference as a measure of RNAPII abundance at each gene? We have been told that this is just not done and for the life of me I don't understand why not. It seems obvious but....I am not a bioinformatician. Many thanks!