introduction to chIP-seq analysis

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This training gives an introduction to ChIP-seq and ATAC-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.


The aim is to:

  • have an understanding of the nature of ChIP-seq and ATAC-seq data
  • perform a complete analysis workflow including QC, read mapping, visualization in a genome browser and peak-calling using Galaxy
  • have an overview of possible downstream analyses
  • perform a motif analysis with online web programs


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.


Swann Floc’hlay