QuestionsCategory: ChIP-Seq Data AnalysisPeak calling and analyses: If the control is input, which method peak calling do you prefer?
stonelakeak@nih.gov Staff asked 5 months ago

If the control is input, which method peak calling do you prefer?

1 Answers
stonelakeak@nih.gov Staff answered 5 months ago

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.