I have a slightly basic question about using DEseq downstream of CCAT -
After calling peaks using CCAT on my tumor and normal samples ( i have 5 such pairs) - Deseq requires a read count in a list of regions (common ?) across conditions ( you want to check for differential peaks in ) . However CCAT has varying regions that it identifies in different samples. So how do I get the read counts for eg. peak regions identified in T1 from the CCAT output of N1 ?