When I call peaks with MACS2, can I use one ChIP (antibody1) as the control for a second ChIP antibody? Can I detect differences between the two proteins that way?
As a general rule of thumb, MACS2 is not designed to handle the direct comparison of two ChIP samples. It only works when one assumes there are no peaks identified in the sample acting as control that are not located in the sample acting as ChIP. MACS2 does have its own differential peak calling tool, but it has been shown to only work with narrow peaks and tends to be very stringent. The one case in which I have successfully used two ChIP samples for a direct comparison in MACS2 is when I had a histone modification like H3K4me2 as a treatment and H3 as the control. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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