Transcriptomics Analysis: RNA-seq

Date 23 - 25 February 2021
Speaker(s) Paolo Angelino, Isabelle Dupanloup
ECTS 0.75
Fees *academic: 180 CHF   -   for-profit: 900 CHF
Cancellation deadline 9 Feb 2021
City Lausanne
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.

This course will take place in Lausanne with rules complying to COVID situation (distances and hygiene). Should the Covid-19 situation in early February be such that physical meetings are not recommended by the Swiss Government, we will switch to a virtual event on the same date, restricted to registered participants only.

Please check that you are not coming from states and areas with an increased risk of infection as applications from these countries will not be accepted for courses held in classrooms.


This three-day course will provide an overview of the RNA-seq analysis pipeline, as well as the downstream analysis of the resulting data using bioconductor packages in R. The course will cover the following topics:

  • The structure of an RNAseq analysis pipeline:
    • Raw data quality check;
    • RNAseq reads alignment;
    • Gene Expression level quantification and normalization by reads counting;
    • De novo Transcripts reconstruction and differential splicing.
  • Overview of downstream analysis
    • Differential Expression analysis with R/Bioconductor packages;
    • Class discovery: usage of Principal Component Analysis, Clustering, Heatmaps, Gene Set Enrichment Analysis in RNA-seq analysis.

Next Generation Sequencing (NGS) techniques will not be covered in this course; experimental design as well as the statistical methods will not be detailed in this course.


Life scientists who are new in the RNA-seq data field but have some R and statistical knowledge.


Knowledge / competencies

  • Participants should already have a basic knowledge of Next Generation Sequencing (NGS) techniques; this course will discuss only the data analysis steps and not the data generation.
  • A basic knowledge in statistics is required. Participants should know about p-values, student T-test, multiple testing correction and classification, PCA.
  • A basic knowledge of R is also required. Participants should know how to read files, run PCA, do classification, visualise heatmaps using R command lines.


Participants should bring their laptop with the latest version of R and Bioconductor installed. There will be access to the eduroam and guest-unil networks.

Learning objectives

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

  • run a RNA-seq pipeline on a small dataset composed of two groups;
  • describe an RNA-seq experimental design;
  • describe pseudo-alignments and alignment software;
  • estimate data quality;
  • normalise counts;
  • know and understand the essential steps of a simple gene expression analysis issued from RNA sequencing;
  • manipulate gene expression matrices and differential expression tables;
  • perform a differential expression analysis based on R/Bioconductor packages (DeSeq2, ...).


9:00 - 10:30 - Introduction to RNA sequencing
10:30 - 10:45 - Coffee Break
10:45 - 12:30 - RNAseq analysis pipeline, part I
12:30 - 13:30 - Lunch Break
13:30 - 15:00 - RNAseq analysis pipeline, part II
15:00 - 15:15 - Coffee break
15:15 - 17:00 - Practicals

9:00 - 10:30 - Differential Expression analysis
10:30 - 10:45 - Coffee Break
10:45 - 12:30 - Differential splicing
12:30 - 13:30 - Lunch Break
13:30 - 15:00 - Practicals
15:00 - 15:15 - Coffee break
15:15 - 17:00 – Practicals

9:00 - 10:30 - Differential Expression analysis with DESEQ2
10:30 - 10:45 - Coffee Break
10:45 - 12:30 - Downstream analysis
12:30 - 13:30 - Lunch Break
13:30 - 15:00 - Practicals
15:00 - 15:15 - Coffee break
15:15 - 17:00 - Practicals


Registration fees are 180 CHF for academics and 900 CHF for for-profit companies. This includes access to course content material.

You will be informed by email of your registration confirmation, and you will be asked to complete the payment of the registration fees within 5 days.

Deadline for registration and free-of-charge cancellation is set to February 9, 2021. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available here.

Venue and Time

This course will take place in Lausanne with rules complying to COVID situation. In the event of new restrictions, it will not be cancelled but streamed for the registered participants.

The course will start at 9:00 and end around 17:00. Precise information will be provided to the participants on due time.

Additional information

Coordination: Monique Zahn, SIB Training Group.

We will recommend 0.75 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.

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For more information, please contact