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.


Lesson Slides Hands-on Time estimation
ChIP-Seq Analysis
01 Download the data
tutorial 15m
01 GenPattern tutorial
tutorial 30m
03 Quality control of the data of the ChIP-Seq training
tutorial 30m
04 Mapping reads with Bowtie
tutorial 15m
05 Peak calling with MACS
tutorial 15m
06 Visualization with deepTools
tutorial 15m
07 Visualizing the peaks in a genome browser
tutorial 15m
08 Motif analysis
tutorial 15m


This material is maintained by:

Alexander Botzki , Janick Mathys , Morgane Thomas-Chollier

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This material was contributed to by:

Morgane Thomas-Chollier , Janick Mathys