Data Analysis of ChIP-Seq Experiments: Common Practice and Recent Developments

In this chapter, we reviewed many aspects of the common workflow for ChIP-Seq data analysis. First, we reminded the readers the potential impact of the design of the ChIP-Seq experiment and the quality of the data on the choice of the tools and the results. Second, we discussed many issues and the common tools in read alignment, peak calling, and the differential enrichment detection. We then proceeded to the discussion on the available analysis pipelines for ChIP-Seq data. Finally, we reviewed the common practice and the new development in allele-specific binding detection, an emergent complementary analysis of ChIP-Seq data that associates this molecular epigenetic phenotype to the variation in the genotype.