I'm validating a MBD-seq library and having difficulty understanding the need for a non-enriched input sample. We're using a MACS based approach to analyse the library, which compares Naive and 4 treatment groups. Someone suggested to me that peaks need to be found relative to input DNA and then compared, but it appears that MACS generates a "local background" to find peaks so input may not be necessary. Could someone explain the benefit of an input sample? I prefer to use the naive profile as a control. Thanks!
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