ChIP-Seq analysis
This training gives an introduction to ChIP-seq data analysis, covering the processing steps starting from the reads to the peaks. Among all possible downstream analyses, the practical aspect will focus on motif analyses. A particular emphasis will be put on deciding which downstream analyses to perform depending on the biological question. This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs.
- Have an understanding of the nature of ChIP-Seq data - Perform a complete analysis workflow including QC, read mapping, visualization in a genome browser and peak-calling - Use the GenePattern platform for each step of the workflow and feel the complexity of the task - Have an overview of possible downstream analyses - Perform a motif analysis with online web programs For this training, we will use a dataset produced by Myers et al [1] involved in the regulation of gene expression under anaerobic conditions in bacteria. We will focus on one factor: FNR. The advantage of this dataset is its small size, allowing real time execution of all steps of the dataset.
Material
Lesson | Slides | Hands-on | Time estimation |
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ChIP-Seq Analysis
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slides | ||
01 Download the data
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tutorial | 15m | |
01 GenPattern tutorial
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tutorial | 30m | |
03 Quality control of the data of the ChIP-Seq training
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tutorial | 30m | |
04 Mapping reads with Bowtie
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tutorial | 15m | |
05 Peak calling with MACS
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tutorial | 15m | |
06 Visualization with deepTools
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tutorial | 15m | |
07 Visualizing the peaks in a genome browser
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tutorial | 15m | |
08 Motif analysis
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tutorial | 15m |
Maintainers
This material is maintained by:
Alexander Botzki , Janick Mathys , Morgane Thomas-ChollierFor any question related to this topic and the content, you can contact us at bits@vib.be
Contributors
This material was contributed to by:
Morgane Thomas-Chollier , Janick MathysReferences
- Bailey et al. : Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9, e1003326 (2013)
- Thomas-Chollier et al.: A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs Nature Protocols 7, 1551–1568 (2012)
- Kevin S Myers et al.: Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet.: 2013, 9(6);e1003565