To support molecular and cell biologists in their quest for autonomy when dealing with bio-informatics, bio-statistics, genomics or systems biology, Pr Sandrine Lagarrigue - supported by Agrocampus Ouest - started offering a highly multidisciplinary and modular workshop dedicated to biologists ten years ago. I joined the teaching staf in 2014 and organize since then 4 yearly training days on sequence bio-informatics and statistical analyses for genomic and epigenomic data.
The workshop dedicated to ChIP-seq analysis address the following topics:
- Introduction to epigenome screening technologies (ChIP-seq, ATAC-seq, MNase-seq …)
- Biases and noise in sequencing data
- Introduction to UNIX environment and Bash scripting
- Work on a cluster with job schedulers (SLURM and SGE)
- Use parallel environments
- Use genomic databases (Ensembl, UCSC)
- Quality check of ChIP-seq data
- Pre-processing and alignment of ChIP-seq data
- Peak calling
- Irreproducible discovery rate
- Use of R Bioconductor for functional genomics
- Normalization strategies for epigenomic assays (RPM, TMM, Lowess)
- Functional enrichment for epigenomic assays
- Motif enrichement analysis
Below, you will find slides from our last ChIP-seq workshop (in french).
Day 1
Day 2
Bioconductor guide for ChIP-seq analysis