Peak calling and analyses: If the control is input, which method peak calling do you prefer?

One of the great things about MACS2 is that it was designed to work with input samples and incorporates the information in a few different ways. One special feature is that it attempts to call peaks in the input relative to the ChIP in order to determine a false discovery rate. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.