I have a number of atacseq bams and their total read numbers differ. I did peak calling with and without --SPMR for normalization and there is no difference between the two ......broad_peaks.broadPeak files. yet there is a difference in the resulting two ....broad_treat_pileup.bdg files. While using callpeak, does --SPMR have no effect on the signalValues? If that is the case, should I do another peak calling from the bdg files?
My end goal is to see what happened to some specific regions, whether they got condensed or decondensed and I cannot make sure whether this read depth difference effect the signalValues.