I've read that when you give MACS an IP file and an input file (-t and -c), the larger library is scaled to the smaller library.
My question is: Do the bdg files (pileup and lamda) reflect this scaling?
I have samples from different conditions and I would like to show the graphs side by side but the library sizes were quite different. Each sample has an IP and an input file, so each sample was run through MACS independently.
My understanding is that each pileup can be considered to be normalized for library size in comparison to the corresponding lambda, but not between different IP samples.... is that correct?