I have recently started analyzing ChIP-seq data. I have two datasets from GEO for two different transcription factors in same sample and want to compare their overlap binding sites and determine genes that are co-regulated by these TFs. I have aligned the two datasets using the same pipeline and have used MACS2 for peakcalling. I was going to use
bedtools intersect to determine the overlapping peaks. Before I proceed, however, I wanted to know whether I should be normalizing for the library size? Typically the data is normalized for Libray size by the statistical method used to detect differential abundances.
In this instance, are these peak numbers comparable to each other as is? If I need to normalize, how can I proceed with it?