Whole transcriptome data analysis – Course and Conference Office

EMBL Course

Whole transcriptome data analysis


Proof of COVID-19 vaccination or recovery is required to attend this on-site course. Please see EMBL’s COVID-19 safety policy for on-site events.

Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

Course overview

This course will teach the biological researchers how to analyse biological data sets using open-source software. Most of the analysis will be performed with docker4seq package, which was developed to facilitate the use of computing demanding applications in the field of NGS data analysis. Docker4seq package uses docker containers that embed demanding computing tasks (e.g. short reads mapping) into isolated containers. This approach provides multiple advantages: the user does not need to install all the software on its local server, the results generated by different containers can be organised in pipelines and reproducible research is guarantee by the possibility of sharing the docker images used for the analysis.

Computers for hands-on exercises will be provided along with demo data sets.


This course was developed for biological researchers as the intended audience. Basic knowledge of massively parallel sequencing (MPS) is desirable, however R-coding skills and deep knowledge of statistics are not necessary.


  • Tools for RNA-seq data analysis
  • Experimental design
  • Quality control
  • Normalisation and data reformatting
  • Basic statistics
  • Selecting differentially regulated genes/microRNAs
  • Selecting alternative splicing events
  • Multiple testing
  • Biological interpretation

Learning outcomes

  • Understand the importance of experimental design in order to ask sensible biological questions
  • Assess the quality of your data
  • Perform normalisation and reformatting procedures
  • Complete basic statistical tests on Next Generation Sequencing (NGS) data
  • Understand some of the problems encountered when analysing data

What past participants say about this course

“My research focus is on RNA sequencing, infectious diseases and next generation sequencing. Attending this course helped me understand the basics, got me career advice and extended my network. Overall, it made me a better researcher.” – Abhay Deep Pandey, Translational Health Science And Technology Institute, India

“Excellent course on the complete spectrum of RNA-Seq. I would highly recommend this course to all biologists.” – Issaac Rajan, King Abdullah University of Science and Technology, Saudi Arabia


Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Date: 21 - 26 May 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


  • Marco Beccuti

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