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ChIP-seq analysis using R

https://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/ChIP-Seq/Bori_Mifsud/README.md

ChIP-seq analysis using R

Keywords

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

Authors

  • Bori Mifsud
  • Kathi Zarnack

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Description

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

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 the tools to do their own preliminary data analysis.

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Prerequisites

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

Target audience

  • Biologist
  • Programming experience

Learning objectives

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

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Materials

  • EMBOOct2014ChIPseqlecture
  • EMBOOct2014ChIPseqpractical
  • EMBOOct2014ChIPseqpracticaltalk

Data

### Description
NFKB ChIP-seq data from Kasowski et al. (2010)
H3K36me3 ChIP-seq data in HepG2 and K562

Availability

www.ebi.ac.uk/~gerle/teaching/Material2014/

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Technical requirements

  1. R-3.1.1 or R-3.1.0, Bioconductor >= 3
  2. BioConductor packages:
    • chipseq
    • GenomicFeatures
    • ShortRead
    • rtracklayer
    • BSgenome.Hsapiens
    • seqLogo DiffBind
  3. MACS2
  4. USeq
  5. SISSR
  6. 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

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

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

Additional information

Authors: Bori Mifsud, Kathi Zarnack