ABSTRACT
This chapter focuses on the R/Bioconductor package ChIPQC that provides a comprehensive Chromatin immunoprecipitation sequencing (ChIP-seq)-specific quality control analysis. ChIP-seq enriches for regions that are bound by the transcription factor or modified histone of interest. One of the most important quality control steps is to check for the presence and types of enriched regions. Most factors will be enriched in one or a few of the following annotated genomic regions: promoters, exons, introns, 5' or 3' untranslated regions (UTRs). This allows for assessing the immunoprecipitation efficiency in the library before peak calling. It is important to check for the level of duplication within the sample. Duplication can be a sign of low quality ChIP-seq samples, as duplicated reads can come from PCR over amplification of libraries with low starting material and therefore low complexity, as well as from blacklisted regions, which are artefacts and should be removed.
