I have some chip-seq data for three different conditions for which I have plotted RPKM normalized counts around features of interest using deeptools. The plot clearly shows differences in chip-signal between the conditions but I am concerned about different levels of backgrounds between conditions. The blue sample in the plot seems to have lower signal than the other two samples no matter which regions I plot.
Any ideas on how I can normalize the samples so the have the same basal signal? I assume some sort of z-score normalisation may work but am not sure how to do it with my bigwig files.