PHINDaccess RNAseq course 2020

Dates, time & location


Day Date Time
1 Monday 10th of February 2020 9:00-16:30
2 Tuesday 11th of February 2020 9:00-16:30
3 Wednesday 12th of February 2020 9:00-16:30
4 Thursday 13th of February 2020 9:00-16:30

Location: Institut Pasteur Tunis


Julia Ponomarenko Sarah Bonnin

from the CRG Bioinformatics core facility in Barcelona, Catalonia, Spain.

Material available at https://biocorecrg.github.io/PHINDaccess_RNAseq_2020/

Learning objectives

At the end of the course, the participants will be able to:

  • Understand the analysis steps from raw reads to expression counts, differential expression and interpretation of DE genes using the gene set enrichment analysis.
  • Find RNA-seq data in public repositories.
  • Define a good experimental design, including sequencing parameters and quality control steps.
  • Perform quality assessment of RNA-seq data, both raw and computed.
  • Understand file formats commonly used in RNA-seq data analysis.
  • Gain an overview on common software tools for RNA-seq data analysis and their limitations.
  • Perform gene differential expression analysis.

Course Program

  • Day 1: Introduction to RNA-seq, experimental design, Start analyzing RNA-seq data: raw data download, quality control, prepare sequencing reads for mapping.
  • Day 2: Read mapping to reference genome/transcriptome, UCSC Genome Browser.
  • Day 3: Refreshing basics in R. Gene differential expression analysis.
  • Day 4: Functional analysis. Independent exercise.


Familiarity with the Linux command line Familiarity with the R language scripting