Topic outline

  • General

    Transcriptomics Analysis: RNA-seq

    Lausanne, 20-21 October 2015

    This course will present all the bioinformatics tools required to analyze RNA-seq gene expression data, from the raw data to the biological interpretation.

    Trainer: Paolo Angelino, SIB / BCF group
    Keywords: RNA, RNA-seq, trancriptome, transcriptomics
    Venue: Classroom 2020, Genopode Building, University of Lausanne (Metro M1 line, Sorge station)
    ECTS: 0.5 (given a passed exam at the end of the course)
    Fee: 100 CHF for academics. Others, please contact us
    Cancellation deadline: 13 October 2015
    Application status: Closed

    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


    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


    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 of the R statistical software ( is also required.

    Technical: Participants should bring their laptop with the R and Virtualbox software installed.


    The registration fees for academics are 100 CHF. This includes course content material and coffee breaks. Participants from non-academic institutions should contact us before applying.

    The course is currently full; another session will take place in the first semester 2016. If you want to be informed when registration opens, make sure you subscribe to our  SIB courses mailing-list.

    Deadline for application and free-of-charge cancellation is set to October 13. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions, available at

    You will be informed by email of your registration confirmation.

    Additional information

    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

    Organiser: Frédéric Schütz (Bioinformatics Core Facility)

    Coordinator:Training & Outreach Group / Grégoire Rossier

  • Programme

    Tuesday October, 20th

    9:15 - 10:30 - Introduction to RNA sequencing

    10:30 - 11:00 - Coffee Break

    11:00 - 11:45 - RNAseq analysis pipeline, part I

    11:45 - 13:00 - Lunch Break

    13:00 - 14:15 - RNAseq analysis pipeline, part II
    14:15 - 15:00 - Practicals

    15:00 - 15:30 - Coffee break

    15:30 - 16:30 - Practicals

    Wednesday October, 21st

    9:15 - 10:30 - Differential Expression analysis

    10:30 - 11:00 - Coffee Break

    11:00 - 11:45 - Differential splicing

    11:45 - 13:00 - Lunch Break

    13:00 - 14:15 - Downstream analysis
    14:15 - 15:00 - Practicals

    15:00 - 15:30 - Coffee break

    15:30 - 16:30 - Practicals