I performed a ChIP-seq experiment in which I'm looking at H3K4me3 levels under three conditions. One condition is a control and the two others are different treatments (treatment1 and treatment2).
I've already aligned my reads to the genome with BowTie2 and called peaks with MACS2 by comparing each individual treatment with it's corresponding control.
I'd really like to find a tool (or set of tools) that will allow me to find peaks that are enriched in treatment1 (when compared to the control) versus treatment2 (when compared to the control) and vise versa...hopefully this makes sense.
I also have three biological replicates per condition so I have a total of nine samples. I assume that having biological replicates will be useful for statistical analysis, but I'm not sure how to make the best use of them.
Any advice would be appreciated!