I have been reading some papers, and some of them make use of GSEA and the associated log fold change to quantify differentially expressed genes. I notice that most of these studies were conducted using RNA-seq, and not in ChIP-seq. My question is the following: do ChIP-seq analysis still make use of such tools for quantification?
I understand that the end goal of ChIP-seq is to find peaks and annotate them, but is there something that I am missing regarding understanding the downstream analysis in ChIP-seq vs RNA-seq?
Thanks a lot for your help!