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

advanced bioinformatics
omics
live training

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

Target Audience:
VIB PhD student
VIB postdoc
VIB staff scientist
VIB group leader or expert
VIB technical support
Location:

Park Inn, Leuven

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.

Learning outcomes

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
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

People who who have no experience with NGS data must follow the 'Introduction to NGS analysis' training.

Trainers

Swann Floc'hlay
VIB-KULeuven Center for Cancer Biology, BE
Swann Floc'hlay is a computational biologist. She obtained a PhD from the Ecole normal supérieure (Paris, France) in the team of Prof. Thieffry in 2020 and joined Prof. Aerts lab in VIB-KU Leuven (Leuven, Belgium) as a postdoctoral researcher in 2020-2022. Her research interests are transcriptional regulation, high-throughput functional genomics and developmental biology.
ORCID

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

Location & Venue

28 October 2022

Leuven - Park Inn by Radisson

Martelarenlaan 36
3010 Leuven
Belgium

Public transport

28 October 2022

Leuven - Park Inn by Radisson
Public transport

The hotel is located 300m from Leuven Central Station, just a short 5 minute walk.

Bike

28 October 2022

Leuven - Park Inn by Radisson
Bike

Bike parking Leuven

Using your bike for longer distances? Check Cycle Highways.

Route description

28 October 2022

Leuven - Park Inn by Radisson
Parking

Underground P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven or parking De Bond, Martelarenlaan 18, 3010 Leuven.

Venue contact

28 October 2022

Leuven - Park Inn by Radisson
Location contact

+32 16 61 66 02

sales.leuven@parkinn.com