In silico in-depth analyses of transcriptomic data with UNIX

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 RNA-seq analysis address 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

Below, you will find slides from our last RNA-seq workshop (in french).


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