ChIPseq annotation with replicates

Question

[Payal]

Hi,

What's the best way to annotate chip peaks in case of replicates? I have 3 replicates each group. I understand Chipseeker is a very convenient tool, but I can't find a clear example of how to merge replicates and annotate the peaks for visualization?

Thanks, Payal

[seidel]

One simple method: reduce all three replicates to a single set of peaks, this will allow you to evaluate the overlap of each replicate with the potential universe of loci observed from your experiment. From this reference you can create a working peak set by only keeping members found in 2 or 3 replicates depending on your stringency requirements.