I have bigwig (RPKM) files of a chip-seq experiment for treatment and control conditions which I am trying to compare. I have 3 replicates for control and 5 replicates for treatment condition. To show the average difference in signal, I merged the replicates for each condition using ucsc bigWigMerge command.
However, if my understanding is correct this command simply adds the signal of all replicates and so the merged treatment file is no longer comparable to the merged control file. The treatment condition has more replicates and so shows higher values than control even when the actual signal shouldn't be different. Is my understanding correct? If yes, is there a way to merge bigwig files using average instead of sum of replicates and does this make sense? (preferably without merging bam files and recreating bigwigs)