ChIP-seq with 2 negative controls

[hersh]

Dear All,

We have ChIP-seq data from one Treatment data set and two negative control data sets (1:- Mock IP and 2:-Input/genomic DNA). We have called peaks for Treatment vs Mock and Treatment vs Input/genomics DNA using MACS. How can we derive final peaks from both datasets.

Are those regions can be called final peaks which are common in both the runs?

[ffinkernagel]

You calculate an 'overlapping' matrix (1 if two peaks overlap, 0 otherwise), and then do an exhaustive mining for the disconnected subsets of the graph.