Introduction to ChIP-Seq data analysis

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# Introduction to ChIP-Seq data analysis

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				<a href="/training-material/hall-of-fame/bebatut/" class="contributor-badge contributor-bebatut"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bebatut?s=36" alt="Bérénice Batut avatar" width="36" class="avatar" />
    Bérénice Batut</a></li>
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## Requirements

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

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)

- [Sequence analysis](/training-material/topics/sequence-analysis)
    - Quality Control: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html)
    - Mapping: [<i class="fab fa-slideshare" aria-hidden="true"></i><span class="visually-hidden">slides</span> slides](/training-material/topics/sequence-analysis/tutorials/mapping/slides.html) - [<i class="fas fa-laptop" aria-hidden="true"></i><span class="visually-hidden">tutorial</span> hands-on](/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html)

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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.](../../images/ecker_2012.jpg)
<small>
[*Ecker et al, Nature, 2012*](https://www.ncbi.nlm.nih.gov/pubmed/22955614)
</small>

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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.](../../images/szalkowski_schmid_2011.jpg)

[*Szalkowski & Schmid, Brief Bioinform, 2011*](https://bib.oxfordjournals.org/content/12/6/626.long)

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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.](../../images/kidder_2011.jpg)

[*Kidder et al, Nature Immunology, 2011*](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541830/)

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## Related tutorials

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
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			<a href="/training-material/hall-of-fame/bebatut/" class="contributor-badge contributor-bebatut"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bebatut?s=36" alt="Bérénice Batut avatar" width="36" class="avatar" />
    Bérénice Batut</a>
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			<a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-badge-small contributor-shiltemann"><img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-badge-small contributor-hexylena"><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/bebatut/" class="contributor-badge contributor-badge-small contributor-bebatut"><img src="https://avatars.githubusercontent.com/bebatut?s=36" alt="Bérénice Batut avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/gallardoalba/" class="contributor-badge contributor-badge-small contributor-gallardoalba"><img src="https://avatars.githubusercontent.com/gallardoalba?s=36" alt="Cristóbal Gallardo avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/nsoranzo/" class="contributor-badge contributor-badge-small contributor-nsoranzo"><img src="https://avatars.githubusercontent.com/nsoranzo?s=36" alt="Nicola Soranzo avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/willdurand/" class="contributor-badge contributor-badge-small contributor-willdurand"><img src="https://avatars.githubusercontent.com/willdurand?s=36" alt="William Durand avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-badge-small contributor-bgruening"><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" /></a></td>
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