Hands on introduction to ChIP-seq and ATAC-seq analysis

Hands on introduction to ChIP-seq and ATAC-seq analysis

Target Audience:

General context

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.

Objectives

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 GenePattern
  • have an overview of possible downstream analyses
  • perform a motif analysis with online web programs
Approach

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.

Required skills

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

Trainers

Morgane Thomas-Chollier

Morgane Thomas-Chollier is a computational biologist and associate professor at Ecole normale supérieure (Paris, France).  She's president of the Société française de Bioinformatique and Junior Member of Institut Universitaire de France. 

Her research interests are transcriptional regulation, high-throughput functional genomics and evo-devo.

Program

9h30 - 11h00: Introduction - Downloading the data

11h15 - 12h30: Quality and stats - Mapping

12h30-13h30: Lunch

13h30-15h00: Peak calling - Visualization

15h15-17h00: Motif analysis - Questions

Practical info

17 February 2020

Park Inn by Radisson Leuven

Martelarenlaan 36
3010 Leuven
Belgium

17 February 2020

Park Inn by Radisson Leuven
Public transport

The hotel is located 300m from Leuven Central Station. The hotel connects to Leuven Central Station by a pedestrian bridge.

17 February 2020

Park Inn by Radisson Leuven
Parking

Park Inn hotel has no own parking. It is possible to park underground in P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven.

17 February 2020

Park Inn by Radisson Leuven
Location contact

+32 16 61 66 02

sales.leuven@parkinn.com

Contact

VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be