Date

November 6-8, 2017

Location

Venue: Universiteit Leiden – Faculty Social Sciences (FSW), Wassenaarseweg 52, 2333 AK Leiden
Room: 1A-21 on November 6 and 8
Room: 1A-37 on November 7

Course coordinators

Peter-Bram ‘t Hoen (LUMC), Leon Mei (LUMC), Jan Oosting (LUMC), Szymon Kielbasa (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. This is an advanced course for people with experience in NGS. The course will consist of lectures, 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 and study design
• Quality control and alignment
• Statistics for differential gene expression
• eQTL analysis and allele specific expression
• Single cell RNA sequencing
• Fusion transcript detection
• Small RNA profiling
• Software for RNA-seq data analysis

Programme

You can find the programme for the course here.

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.

NB: The practicals are mostly in R. We expect that participants have at least basic knowledge of R and experience in running R scripts. If you don’t have any experience with R yet but would like to follow this course, please read some online introductory material about R. For example, http://www.datacarpentry.org/R-genomics/00-before-we-start.html and http://www.datacarpentry.org/R-genomics/01-intro-to-R.html

Participants must bring own laptops capable of running RStudio. Please download and install RStudio before the course. For Galaxy tutorial, please install firefox or google chrome web browser.

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-Connect and BBMRI-NL.

This tutorial should give R novices sufficient knowledge to do the practicals
https://www.nceas.ucsb.edu/files/scicomp/Dloads/RProgramming/BestFirstRTutorial.pdf