Transcriptomics Analysis: RNA-seq

Date 4 - 5 April 2017
Speaker(s) Paolo Angelino
ECTS 0.5
Fees *academic: 100 CHF   -   for-profit: 0 CHF
Cancellation deadline 28 Mar 2017
City Lausanne
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.


This two-day course will discuss the following topics:

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


Any person who has to analyse RNA-seq data.

Learning objectives

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

  • know and understand the essential steps of a Gene Expression analysis by RNAseq, from raw data to a gene expression matrix
  • run a simple RNA seq pipeline
  • perform a Differential Expression analysis based on R/Bioconductor packages



  • 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 of the R statistical software ( is also required.

TechnicalParticipants should bring their laptop with the R and Virtualbox software installed.


Tuesday 4 April
9:00 - 10:30 - Introduction to RNA sequencing
10:30 - 10:45 - Coffee Break
10:45 - 12:00 - RNAseq analysis pipeline, part I
12:00 - 13:00 - Lunch Break
13:00 - 15:00 - RNAseq analysis pipeline, part II
15:00 - 15:15 - Coffee break
15:15 - 17:00 - Practicals

Wednesday 5 April
9:00 - 10:30 - Differential Expression analysis
10:30 - 10:45 - Coffee Break
10:45 - 12:00 - Differential splicing
12:00 - 13:00 - Lunch Break
13:00 - 15:00 - Downstream analysis
15:00 - 15:15 - Coffee break
15:15 - 17:00 - Practicals


Please note that this course is over subscribed.

Deadline for free-of-charge cancellation is set to March 27. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available at

You will be informed by email of your registration confirmation.


University of Lausanne, Genopode building, classroom 2020 (Metro M1 line, Sorge station)

Additional information

Coordination: SIB Training Group

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