This course is aimed at researchers who would like to learn about the analysis of genome-wide profiling of histone modifications, transcription factors (TF) binding and chromatin accessibility, using the ChIP-seq and ATAC-seq techniques. It will alternate theory and hands-on sessions in order to perform an analysis from sequencing data to graphical representations and biological interpretation of the data. It will provide a general introduction on epigenetics and epigenomics, describe the experimental techniques that have been developed to query the epigenome, as well as the bioinformatic and statistical aspects of the analysis.
The practical sessions will include all the steps that will enable the participants to perform a complete data analysis: sequencing quality control, mapping, assessment of ChIP-seq and ATAC-seq specific quality metrics, reproducible peak calling, differential binding/marking, visualization and functional analysis including peak annotation, motif-based analysis and integration with public datasets. The last day of the course will be dedicated to an advisory session, allowing students to discuss further with the teaching team the issues they have encountered during the week.
Getting acquainted to the tools, methods and paradigms underlying research in gene regulation and epigenomics
Understanding and applying the appropriate controls and normalization methods for quantitative epigenomic analysis.
Knowing the standard programs and pipelines to analyze epigenomic data, from raw sequencing reads to peak annotation.
09-13 May 2022
Postgraduate students, postdocs, engineers and researchers interested in epigenomics, epigenetics and the regulation of gene expression.
PLACE OF THE TRAINING
Institut Pasteur de Tunis.
Institut Pasteur Paris team
SPEAKERS & AFFILIATIONS
- Rachel Legendre (Institut Pasteur, Paris)
- Hélène Lopez-Maestre (Institut Pasteur, Paris)
- Victoire Baillet (Institut Pasteur, Paris)
- Claudia Chica (Institut Pasteur, Paris)
Basic knowledge of command line (undrstanding how to run a program, how to change between directories)