Course: RNA-seq data analyses

General information

  • Next occasion: October 30 – November 1, 2013
  • Keywords: Next-generation sequencing, NGS, data analysis, RNA-seq, transcriptome
  • Location: Pieter de la Courtgebouw, Wassenaarsweg 52, Leiden, The Netherlands
  • Organiser: LUMC & NBIC
  • Coordinators: Peter-Bram ‘t Hoen (LUMC), Celia van Gelder (NBIC), Marieke Simonis (UU)
  • Website:


NBIC and partner LUMC is organizing a 3-day course on RNA-seq data analysis from October 30 – November 1st, 2013. This is an expert course for people with experience in NGS and a follow-up course on the general NBIC NGS data analysis course (which will be given from 28-30 August 2013 in Rotterdam). The course will consist of seminars and hands-on command line, Galaxy and R practicals and will focus on data preprocessing, quality control, alignment, visualization and statistics for differential transcript expression. 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
  • Small RNA profiling
  • Software for RNA-seq data analysis

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. We will mainly use command line tools in the course. Participants are expected to familiarize themselves with the command line and with R before the start of the course. Instruction material will be sent in advance. 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 project RD-Connect and Marie Curie European Training Network TranCYST.


Link to course programme RNA-seq


You can register for this course and find information about the fee on the enrolment page.[LINK]

Information about 2012 edition of this course

Lecture notes (slides) of the 2012 RNA-seq data analyses course in Nijmegen

Genomic Resequencing advanced NGS course lectures by NBIC are licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. Based on a work at NBIC.

Monday October 15th

 Tuesday October 16th

Sample Data to repeat this days R-tutorials can be found here

Wednesday October 17th