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ChIP-seq analysis using R - Practical

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ChIP-seq analysis using R - Practical

Keywords

ChIP-Seq, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming

Authors

  • Bori Mifsud
  • Kathi Zarnack

Type

  • Both

Description

ChIP-seq is the most commonly used technique to study binding profiles of chromatin proteins, such as TFs or histone modification patterns. This practical is an introduction to ChIP-seq data analysis mainly using R, some command line based peak-callers and online software. It provides means to perform peak calling, annotation, motif search and differential binding analysis.

Aims

The aim of the practical is to enable experimental or computational biologists to perform preliminary analysis on their ChIP-seq data and to give them an overview of the workflow.

Prerequisites

  • R-programming
  • Unix
  • HTS-introduction
  • Preprocessing
  • Alignment

Target audience

  • Biologist
  • Programming experience

Learning objectives

  • Describe and perform steps of the ChIP-Seq workflow
  • Visualise raw and processed data
  • Annotate and interpret results

Materials

  • EMBOOct2014ChIPseqpractical
  • EMBOOct2014ChIPseqpractical_talk

Data

Timing

~ 4 hours

Content stability

Stable. There might be small updates in the future.

Technical requirements

  • R-3.1.1 or R-3.1.0, Bioconductor >= 3
  • BioConductor packages:
    • chipseq
    • GenomicFeatures
    • ShortRead
    • rtracklayer
    • BSgenome.Hsapiens
    • seqLogo
    • DiffBind
  • MACS2
  • USeq
  • SISSR
  • optional: IGB

Literature references

  • Kasowski et al., Variation in transcription factor binding among humans. Science. 2010 Apr 9;328(5975):232-5. doi: 10.1126/science.1183621

Keywords: ChIP-Seq, Peak-calling, Differential-binding, Visualisation, Annotation, Homo-sapiens, R-programming

Authors: Bori Mifsud, Kathi Zarnack

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