Can you talk a little bit about IDR? Is IDR something you must do for transcription factor ChiP-seq or is it optional? What about with histone marks? Does IDR work with MACS2 outputs?
IDR or Irreproducible Discovery Rate is a tool developed by the ENCODE team to measure consistency between two replicates. Typically, called peaks, including those generated by MACS2, are sorted and ranked by q-value (or signal-value) then parsed to IDR to assess reproducibility. In our experience, IDR is (a) a bit too stringent when applied to narrow peaks [most transcription factors], (b) works only for a pair of replicates and (c) sometimes abruptly fails for some cases like broad peaks [most histones] or too few peaks in one replicate or both replicates. Hence, we have not generalized its utilization by incorporating it in our pipelines. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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