We performed ChIPseq experiments on two treatment groups with ~8 replicates each. We did some genome-wide comparisons, called peaks, used the DiffBind R package for analysis of differentially enriched regions, etc. Finally, we have come up with some genes of interest of which we would like to compare the signal around the TSS between the two groups.
I have done this using deepTools multiBamSummary, providing a BED file with the regions of interest. However, as far as I understood, this does not normalize the data (which would makes sense since its made to report the read coverage).
Do you know a tool that can do the same, just with a normalization step, or would you do something else instead? INPUT is not available.