Hi,

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.
Whether you use the SPMR flag or not, MACS2 will normalise the data internally to call peaks. The SPMR flag only effects the signal track produced. With the flag present the signal will be normalised to reads per million, this is for comparison with other samples which have been sequenced to different read depths.