ChIP-seq analysis using R - Experimental design and peak calling.

Keywords

ChIP-Seq, Experimental-design, Peak-calling, Visualisation

Authors

• Bori Mifsud
• Kathi Zarnack

Type

• Lecture

Description

This lecture is an introduction to ChIP-seq experiments and data. It provides a theoretical background to experimental design and peak calling.

Aims

The aim of the course is to draw biologists' attention to the impact of experimental design, and the pitfalls of ChIP-seq data analysis, and to give them an overview of the analysis steps.

Prerequisites

• HTS-introduction
• Preprocessing
• Alignment

Target audience

• Biologist
• Computational biologist

Learning objectives

• Define appropriate experimental design
• Describe and perform steps of the ChIP-Seq workflow
• Explain how peak callers work

Materials

• not applicable

Data

• not applicable

Timing

1 hour

Content stability

Stable. There might be small updates in the future.

Technical requirements

• None

Literature references

• Landt et al., ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.
• Chen et al., Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985.