This repository will serve as a well of information, all regarding the analysis of ChIP-Seq experiments. I will try to include here tools I would like to test, sources of information regarding analysis and everything I can think of related to RNA-Seq.
https://github.com/crazyhottommy/ChIP-seq-analysis - This github repository contain a lot of information, all regarding the analysis of ChIP-Seq experiments. Each of the steps during the analysis has its own section. very good and informativ.