Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations.

Abstract

ChIP-Seq is used to study DNA-protein interactions, unraveling chromatin states and gene regulatory properties of transcription factors. ChIP-Seq involves immunoprecipitation followed by sequencing using Next-Generation sequencing approaches. The ENCODE consortium provides extensive guidelines for ChIP-Seq analysis. Meanwhile, appropriate QC metrics and knowledge to interpret outcomes are essential for a good ChIP-Seq experiment. This chapter outlines the various QC metrics and analytical tools for ChIP-Seq analysis to provide a better understanding of the results.