Introduction to RNA-Seq: From quality control to pathway analysis

Date 1 - 2 September 2022
Speaker(s) Wandrille Duchemin
ECTS 0.5
Fees *academic: 120 CHF   -   for-profit: 600 CHF
Cancellation deadline 14 Aug 2022
City Basel
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.


This two-day course will present the theory and bioinformatics tools required to analyze RNA-seq gene expression data, The course will present the theory and bioinformatics tools required to analyse RNA-seq gene expression data, from the raw data until the biological interpretation. The following topics will be discussed:

  • Quality control
  • Mapping to genomes & transcriptomes
  • Read counting, gene & exons differential expression analysis
  • GO enrichment and pathway analysis


This course is addressed to life scientists or bioinformaticians familiar with "Next Generation Sequencing" who wish to acquire the necessary skills to analyse RNA-seq gene expression data.

Learning outcomes

At the end of the course, the participants are expected to:

  • Describe advantages and pitfalls of RNA sequencing
  • Design their own experiment
  • Perform the downstream analysis using command line software (QC, mapping, counting, differential expression analysis, pathway analysis, etc)
  • Critically assess the quality of their results at each step of the downstream analysis


Knowledge / competencies

Participants should already have a basic knowledge in Next Generation Sequencing (NGS) techniques.

Basic knowledge of the R statistical software and completion of an introductory course on UNIX (eg UNIX fundamentals) or equivalent knowledge is also required.


You are required to have your own Wi-Fi enabled laptop.

You should also have access to a terminal on your computer: if you are on macOS / Linux, this is already the case; if you are on Windows, you should install a terminal which lets you do ssh (for instance mobaXterm).


This course will be held in Basel.

The course will start at 9:00 and end around 17:00.

Precise information will be provided to the participants in due time.


The registration fees for academics are 120 CHF and 600 CHF for for-profit companies.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Deadline for free-of-charge cancellation is set to 14/08/2022. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Additional information

Coordination: Diana Marek, SIB Training Group.

We will recommend 0.5 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact