Transcriptomics Analysis: RNA-seq

Date 11 - 13 February 2020
Speaker(s) P. Angelino
ECTS 0.5
Fees *academic: 120 CHF   -   for-profit: 600 CHF
Cancellation deadline 28 Jan 2020
City Lausanne
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.


This two-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.

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;
  • know about RNA-seq experimental design;
  • know about pseudo-alignments and alignment software;
  • be able to check for data quality;
  • be able to normalise counts;
  • know and understand the essential steps of a simple gene expression analysis issued from RNA sequencing;
  • be able to manipulate gene expression matrices and differential expression tables;
  • be able to perform a differential expression analysis based on R/Bioconductor packages (DeSeq2, ...).

Tentative schedule

Day 1: RNA sequencing pipeline
9:00 - start of the day
10:30 - 10:45 - Coffee Break
12:00 - 13:00 - Lunch Break
15:00 - 15:15 - Coffee break
17:00- End of the day

Day 2: Differential Expression analysis using R/biocondoctor packages
9:00 - start of the day
10:30 - 10:45 - Coffee Break
12:00 - 13:00 - Lunch Break
15:00 - 15:15 - Coffee break
17:00- End of the day


Registration fees are 120 CHF for academics and 600 CHF for for-profit companies. This includes course content material and coffee breaks.

Deadline for free-of-charge cancellation is set to 28 January. 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.

You will be informed by email of your registration confirmation.

Venue and Time

University of Lausanne, (Metro M1 line, Sorge station), interactive map.

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: Patricia Palagi, 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.

For more information, please contact