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Introduction to ChIP-Seq data analysis

Bérénice Batut

Updated: PURL: gxy.io/GTN:S00059

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Requirements

Before diving into this slide deck, we recommend you to have a look at:

Introduction to Galaxy Analyses

Sequence analysis
- Quality Control: slides slides - tutorial hands-on
- Mapping: slides slides - tutorial hands-on

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What is ChIP sequencing?

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Where my data comes from?

Cartoon showing the histones forming part of the chromosome. Various insets zoom in from the DNase I hypersensitive sites to DNA with transcription factors and binding sites, which zooms into a block diagram of a gene. Ecker et al, Nature, 2012

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Chromatin immuno-precipitation

Cartoon of Chromatin immuno-precipitation. DNA interacts with proteins, this is cross-linked and sheared into DNA-protein complexes, immunoprecipitated, purified, and the bound DNA is sequenced. This is then mapped to a reference genome and the tag distribution is plotted along a chromosome.

Szalkowski & Schmid, Brief Bioinform, 2011

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How to analyze ChIP-seq data?

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Common procedures for ChIP-seq data analysis

Complex graphic with the first step being Sequence alignment. Then Inpsect data quality with several substeps and graphics shown genome browser, motifs, and a chart of tag density vs tss. Lastly is peak calling, for broad peaks CCAT and SICER, for Sharp peaks MACS, and for both ZINBA.

Kidder et al, Nature Immunology, 2011

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Thank You!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Author(s)	Bérénice Batut
Reviewers

Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.

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Introduction to ChIP-Seq data analysis

Requirements

What is ChIP sequencing?

Where my data comes from?

Chromatin immuno-precipitation

How to analyze ChIP-seq data?

Common procedures for ChIP-seq data analysis

Related tutorials

Thank You!

Requirements

Help