Hello everyone! I have a question about a histone marks ChIP-seq experiment. When I normalized my samples with RPKM or TMM, I realized WT condition has a higher signal everywhere (background and peaks detected by macs2). So although the signal-to-noise ratio is lower than the mutant condition, the signal in the peaks is higher, even in regions I had checked by RT-qPCR before sequencing. I was wondering If there is a way to normalize the samples according to the background of each one, or any normalization method to solve this problem.

Thanks in advance!

The csaw user guide has a detailed discussion of normalizing ChIP-seq samples, as does the DiffBind vignette. Those would be good places to start.