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# Introduction to ChIP-Seq data analysis
Authors:
Bérénice Batut
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Updated: Jul 9, 2021
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??? Presenter notes contain extra information which might be useful if you intend to use these slides for teaching. Press `P` again to switch presenter notes off Press `C` to create a new window where the same presentation will be displayed. This window is linked to the main window. Changing slides on one will cause the slide to change on the other. Useful when presenting. --- ## 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: [
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slides](/training-material/topics/sequence-analysis/tutorials/quality-control/slides.html) - [
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hands-on](/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html) - Mapping: [
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hands-on](/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html) --- # What is ChIP sequencing? --- ### 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> --- ### 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) --- ## How to analyze ChIP-seq data? --- ### 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/) --- ## Related tutorials --- ## 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!
Authors:
Bérénice Batut
This material is licensed under the Creative Commons Attribution 4.0 International License
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