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 staff in 2014 and have since contributed to yearly training days on sequence bio-informatics and statistical analyses for genomic and epigenomic data.
The workshop dedicated to RNA-seq analysis addresses the following topics:
- 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 RNA-seq data
- Pre-processing and alignment of RNA-seq data
- Variant calling on RNA-seq data
- Infer transcript models from RNA-seq data
The course is designed for biologists who need to understand the logic of RNA-seq analyses even when they are not full-time bioinformaticians. I therefore emphasize the relationship between experimental design, biological replication, sequencing depth, quality control, mapping strategy and interpretation of downstream results.
At more advanced levels, this teaching can be extended toward differential expression, dimensionality reduction, functional enrichment and the construction of a coherent scientific narrative from RNA-seq figures such as PCA plots, heatmaps and volcano plots.
Below, you will find slides from our last RNA-seq workshop (in french).