ChIP-seq: To use IDR, samples have to pass both tests or is it enough to pass the pseudo-replicate test?
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3.8 years ago
salamandra ▴ 460

In order to use IDR threshold to select consistent peaks between two replicates of ChIP-seq, samples have to pass the pseudo-replicate consistency test (Np/Nt < 2). My samples passed that test, but failed the self-consistency test (N1/N2 = 2.5 > 2), which is also mentioned by ENCODE. To use IDR, samples have to pass both tests or is it enough to pass the pseudo-replicate test?

ChIP-Seq IDR • 1.3k views
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