ABSTRACT
This chapter presents the different types of Chromatin immunoprecipitation sequencing (ChIP-seq) signals and how these affect the identification of peaks. It describes the general strategy employed by most peak callers, and introduces several existing tools and their specific features. The chapter provides example code for peak calling on ChIP-seq data for a transcription factor (TF) and a histone mark. Peak calling is the core of each ChIP-seq data analysis pipeline as it identifies the genomic regions occupied by the TF or histone mark of interest. The number of peaks found by different peak calling methods is highly dependent on the thresholds and parameters used, and should therefore be considered with caution. Peak callers typically merge close peaks into large regions, which may result in a loss of resolution. Therefore, it is important to separate the two types of regions examined by ChIP-seq: broad versus sharp.
