I'm trying to visualize differences in H3K9ac binding between treatment and control groups for a certain project through visualizing the profile plots, but the provided files are only BED files with significant peak coordinates, raw SRA runs and a couple of BigWig files per sample (2 replicates for each). The BigWig files seem to be the output of MACS2. For each sample, there's a *_treatment_pileup.bw and a *_control_lambda.bw file. For what I understand, the *_treatment_pileup.bw files shows peaks that are not corrected for input/genomic background signal. If that's correct, is it valid to use bigWigCompare to perform that correction between each treatment and input file for each sample? If so, which type of correction would be preferable, log2 or subtraction? And, lastly, how should I go about normalizing the output of bigWigCompare (e.g., to avoid negative values)?
