Hey All,
I have 2 biological replicates for a treatment chip seq experiment. When I analyze these 2 replicates independently (using MACS 1.4.2) I get about 3000 peaks identified for both replicates however when I merge them together I only get about 2000. How exactly does merging the replicates together change how MACS identifies peaks?
Any help would be appreciated
Leanne
I have 2 biological replicates for a treatment chip seq experiment. When I analyze these 2 replicates independently (using MACS 1.4.2) I get about 3000 peaks identified for both replicates however when I merge them together I only get about 2000. How exactly does merging the replicates together change how MACS identifies peaks?
Any help would be appreciated
Leanne
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