Practical Guide to ChIP-seq Data Analysis
Focus Computational Biology Series

Chromatin immunoprecipitation sequencing (ChIP-seq), which maps the genome-wide localization patterns of transcription factors and epigenetic marks, is among the most widely used methods in molecular biology. Practical Guide to ChIP-seq Data Analysis will guide readers through the steps of ChIP-seq analysis: from quality control, through peak calling, to downstream analyses. It will help experimental biologists to design their ChIP-seq experiments with the analysis in mind, and to perform the basic analysis steps themselves. It also aims to support bioinformaticians to understand how the data is generated, what the sources of biases are, and which methods are appropriate for different analyses.

Chapter 1 Introduction to ChIP-seq

Chapter 2 Getting Started

Chapter 3 General Quality Control

Chapter 4 Genomic Alignment

Chapter 5 ChIP-seq-specific Quality Control

Chapter 6 Peak Calling

Chapter 7 Data visualisation

Chapter 8 Comparative Analysis

Chapter 9 Downstream Analyses

Borbala Mifsud is an assistant professor in Epigenomics at the Hamad Bin Khalifa University, Doha, Qatar. She is a computational biologist with a background in molecular biology and works on 3D chromatin conformation and the integration of epigenomic data.

Kathi Zarnack is a principal investigator in Computational RNA Biology at the Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Germany. She is a computational biologist with a background in molecular biology and broad experience in analysing high-throughput sequencing data.

Anaïs F Bardet is a tenured researcher at the National Center for Scientific Research (CNRS) at the University of Strasbourg, France. She is a computational biologist and develops projects exploring the regulation of transcription factor binding.