Tutorial: RNA-seq data analysis using Chipster

January 20, 2015, at 13.00 - 16.00

Computer room A4:214, Uppsala Biomedical Center (BMC)

Course leader: Eija Korpelainen, CSC - IT Center for Science, Finland

Course contents

This hands-on tutorial covers RNA-seq data analysis from quality control (FastQC and PRINSEQ), alignment (TopHat) and quantification (HTSeq) to differential expression analysis (edgeR and DESeq) and genome browser visualization. You will also learn how to save your analysis pipeline as an automatic workflow which can be reused and shared. The user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required, and the tutorial is thus suitable for everybody. The slides are available here.

Participants may bring their own laptop or work on the workstations in the classroom. Please note that if you bring your own laptop, you should have Java 1.7 or newer and Java Web Start installed. You can test beforehand that Chipster starts on your computer by launching the client at http://chipster.csc.fi/ and logging in as guest.

The tutorial is free of charge but requires registration. Update: The Chipster tutorial is now fully booked.

How to find the computer lab

A map over BMC is available. Go to the A5 hallway, up one stair and you need to be let in through the door (Martin Dahlö will open door with his access card).

Host: Ola Spjuth (ola.spjuth@farmbio.uu.se) SciLifeLab and UPPMAX

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Topic revision: r5 - 2015-01-19 - EInfraMPS2015Org
 
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