ABSTRACT
This chapter introduces how to quickly compare chromatin immunoprecipitation sequencing (ChIP-seq) samples by overlapping peaks and how to use a more quantitative approach based on read densities within peaks to investigate differential binding. Comparative analysis of ChIP-seq data is essential to compare the binding of a protein of interest either between replicate experiments or under different physiological conditions. Every comparison in ChIP-seq analysis strongly depends on the thresholds that were applied during the peak calling step. At the level of read densities, the most simplistic approach to assess the overall similarity between samples is to globally correlate their read densities. To compare the read densities specifically in peak regions, a Pearson correlation coefficient can be calculated only within regions that contain a peak in at least one of the samples. The identification of peak regions with differential enrichment is conceptually similar to the identification of differentially expressed genes, as both rely on the comparison of read counts.
