NGS Course: RNA-seq data analysis 2016 (6th edition)


Last edition: September 26-28, 2016


Leiden University Medical Center, The Netherlands

Course coordinators

Peter-Bram ‘t Hoen (LUMC), Jan Oosting (LUMC) and Celia van Gelder (BioSB)

Course description

The BioSB research school and partner LUMC are organizing a 3-day course on RNA-seq data analysis from September 26-28, 2016. This is an advanced course for people with experience in NGS. The course will consist of seminars and hands-on command line, Galaxy and R practicals and will cover the analysis pipelines for differential transcript expression and variant calling. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects.

Course topics

– RNA-seq experimental approaches
– Alignment and de novo assembly
– Statistics for differential gene expression
– eQTL analysis and allele specific expression
– Variant calling and RNA editing
– Fusion transcript detection
– Small RNA profiling
– Software for RNA-seq data analysis


You can now find the final programme here (PDF file)

Target audience

Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. The practicals are mostly in R. We require that participants have at least basic knowledge of R and experience in running R scripts.Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded projects RD-ConnectNeuromicsEurenomics  and BBMRI-NL.

This tutorial should give R novices sufficient knowledge to do the practicals

Travel and lodging

Hotel arrangements have been made with the IBIS hotel at walking distance (3 minutes walk) of the Leiden University Medical Center. Rooms are guaranteed till July 29th, 17h CET. Please note that after that time, rooms are subject to availability.

IBIS hotel, Stationsplein 240-242, 2312 AR Leiden, The Netherlands

Room prices
Room (single use): 83,00 euro & room (double use): 91,00 euro. Prices are including breakfast, excluding tourist taxes.

To book a room at the IBIS hotel, please contact the hotel by email ( or phone (+31 – (0)71 516 00 02) and mention reference code LUMC250916.

In case of questions regarding the hotel reservations, please contact Anita Remmelzwaal (LUMC, email:


Registration is closed, you can express your interest for next year’s course by filling out the pre-registration form.

Previous editions

2015 edition webpage
2014 edition webpage

2013 edition webpage