I am working with MNase-seq data. I have few replicates from samples. For the analysis, I have to work on distogram (histograms of distances between mapped reads’ start positions aligning in opposing orientation), phasogram (histograms of distances between mapped reads’ start positions aligning in the same orientation) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212987/ and few more parameters.
Question: Since all these analysis can be done on each bam files, is it OK to merge the bam files from replicates to get the mean value? If it is OK then how to merge these bam replicates?