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

Keywords

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

Authors

• Anna Poetsch
• based partially on material from Bori Mifsud

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
• Alternative analysis methods to peak calling

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

• Park et al., 2009, ChIP-seq:advantages and challenges of a maturing technology. Nat. Rev. Genet. 10:669
• Pepke et al., 2009, Computation for ChIP-seq and RNA-seq studies. Nat. Methods 6:522
• Laajala et al., 2009, A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
• Wilbanks & Facciotti, 2010, Evaluation of algorithm performance in ChIP-seq peak detection, PLoS One 5:e11471
• Egelhofer et al., 2011, An assessment of histone-modification antibody quality. Nat. Struct. Mol. Biol. 18:91
• Rye et al., 2011, A manually corated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs. Nucleic Acid Res. 39:e25
• Landt et al., 2012, 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., 2012, Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985.
• Li et al., 2009, Measuring the reproducibility of high-throughput experiments. Annals of Applied Statistics
• Filion et al.,2010, Systematic Protein Location Mapping Reveals Five Principle Chromatin Types in Drosophila Cells.