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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The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
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