Transcriptomics Analysis: RNA-seq

Date 25 - 26 April 2018
Speaker(s) Paolo Angelino, Mauro Delorenzi
ECTS 0.5
Fees *academic: 120 CHF   -   for-profit: 0 CHF
Cancellation deadline 16 Apr 2018
City Lausanne
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.

The course is full with a long waiting list.


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


The course is full with a long waiting list.

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 16 April. 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.


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

Additional information

Coordination: Diana Marek, SIB Training Group

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