Hands-on introduction to ChIP-Seq analysis

Trainer Morgane Thomas-Chollier


The aim is to:

  • 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 command line and open source software for each 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


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.


Skills required to follow this training include basic knowledge of Illumina NGS read structure, basic Linux command line understanding. People who lack these skills can follow the 'Introduction to NGS analysis' training.

BITS provides 15 laptops for their training sessions. Depending on the number of participants (max 20), it might be that you have to share the laptop with one other participant but you can also choose to bring your own Linux laptop for this training session.


See the TRAINING AT VIB website for a detailed schedule of this training.

Training material

There is no training material available for this course.


Scientific topics ChIP-seq, Mapping, Sequence quality control, Peak calling, Genome visualisation
Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians