Course preparations

Installation of laptops

For most of the course, we will make use of a virtual machine (VM) running on your laptop (or on the laptop that is provided to you in case you do not bring your own). The VM will be handed to you during the course on a USB stick. To run the VM, you can make use of virtual box software. Virtual box needs to be installed on your laptops. Please do this before the course!
VirtualBox is used to run operating systems in a special environment, called virtual machine, on top of the existing operating system. The virtual machine needs lots of memory. Ideally your laptop should have at least 4 gb of RAM.
VirtualBox can be downloaded from its website:
Installation depends on host operating system. Please follow instruction here:
The VirutalBox user manual can be found here:

Introduction to command line scripting and R

When you are not familiar with working from the command line, please consult this tutorial and carefully work through all the commands in this cheat sheet (borrowed from our scripting course).
When you are not familiar with working with R, please consult the tutorials mentioned in this R introduction document. Download the html document if link does not automatically display in browser.


The final program of the course is available here.

Course material (lectures and practicals)

Day 1

Introduction lecture (Peter-Bram 't Hoen)
Biases in RNAseq lecture (Perry Moerland)
QC lecture (Peter-Bram 't Hoen)
RNA-seq alignment and transcript quantification (Bowo Arindrarto)

Answers practical 1 (Bowo Arindrarto)

Day 2

Small RNA profiling (Youri Hoogstrate)
Location of Youri's small RNA reference

Fusion transcript detection in cancer (David van Ijzendoorn)
Statistical tests for differential expression in count data and pathway analysis (Jelle Goeman)
Testing groups of genes (Jelle Goeman)

Practical 1

Answers of cummeRbund practical (Sander van der Zeeuw)

Practical 2

[Example markdown report] (Jan Oosting)
[Output of markdown report] (Jan Oosting)

Day 3

[Variant calling in RNAseq data, eQTL analysis and allele-specific expression] (Lude Franke)

Allele specific RNA-Seq: The Case of X-inactivation (Hendrik Marks)

Single cell analysis (Anna Alemany Arias)

The Future of RNA Sequencing (Yahya Anvar)

Further reading

Last modified 2 years ago Last modified on Sep 28, 2016 2:54:31 PM

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