Course: NGS Data Analysis in Galaxy (VUmc/CTMM-TraIT course)

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Course: NGS Data Analysis in Galaxy (CTMM-TraIT course)

Date: 19 January 2016, 10:00-17:00
Location: VU University Medical Center Amsterdam, Medical Faculty
building, room MF-H161 (morning) and MF-BK50 (afternoon),

Registration for waiting list: (via Google web form)

Course Organizers: Christian Rausch (VUmc), Youri Hoogstrate (ErasmusMC), Rita Azevedo (CTMM-TraIT).

The program consists of a lecture part in the morning with an introduction to Galaxy, RNAseq based differential gene expression analysis and DNAseq based genomic variant analysis. All three topics are also covered in the hands-on session in the afternoon.

Galaxy is an open, web-based platform that provides access to hundreds of bioinformatics tools for data intensive biomedical research (main focus is on Next Gen sequencing data).
The system is developed by teams at the Penn State and Johns Hopkins Universities, along with thousands of contributions from the world-wide Galaxy community. For more information see:

CTMM-TraIT has set-up a local Galaxy server for Dutch translational biomedical research.
For further questions regarding the TraIT-Galaxy platform, including requests for usage, please read further on the CTMM-TraIT Galaxy page or contact the CTMM-TraIT ServiceDesk at

For users from the VUmc-Cancer Center Amsterdam, the Drylab ( has also setup a local Galaxy server at Accounts can be requested via Christian Rausch (c DOT rausch AT

In this 1-day course you will learn:
* How to use the Galaxy platform (Galaxy 101)
* How to analyze differential gene expression using RNA sequencing data as well as
* How to analyze germline and somatic variants from DNA sequencing data (e.g. Exome sequencing).

Program details:

  • Galaxy 101: Introduction to galaxy (approx. 1:30h)
  • Introduction to Bioinformatics of NGS data analysis and variant calling from DNA sequencing reads (lecture and hands-on, total approx. 2 h).
    The user learns theoretically and practically how to get from raw sequencing reads to genomic variants and how to annotate them using public databases like dbSNP, Clinvar, 1000 genomes etc.
  • Basic RNA Seq and expression analysis (approx 1:00h)
    The user learns how to extract expression profiles from alignments and to do differential gene expression analysis.

Major tools discussed and used during this workshop are Tophat2, FeatureCounts, EdgeR, BWA-MEM, Varscan2, and Annovar.

Please register for this course here.

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