1. Erasmus
Andrew Stubbs

2. Overview Topics Learning Objectives Galaxy applied to RNA and DNAseq
Pathogenic Variant Detection
Cancer Analysis
Learning Objectives
Use of Galaxy
Understanding of NGS analysis
Use and sharing of Galaxy workflows

3. Course Presenters & Organizers
Saskia Hiltemann
Youri Hoogstrate
David van Zessen
Guido Jenster
Andrew Stubbs
Sylvia de Does
Frank van Vliet
Joris Lenstra

4. Resources Galaxies Training Material
Main Penn state:
TraIT Public Galaxy:
IGGalaxy:
Training Galaxy:
Training Material
During course:
After Course End:
Translational Bioinformatics Wiki

5. Course Outline Time Description Presenter
09:00 Welcome and Agenda Andrew Stubbs
09:05 LECTURE: Cancer analysis from Research Scientist to CTMM TraIT Guido Jenster
09:30 LECTURE: Galaxy 101: Introduction to Galaxy Saskia Hiltemann
09:45 PRACTICAL: Galaxy 101: Introduction to Galaxy Saskia Hiltemann / Andrew Stubbs
11:00 BREAK
11:15 LECTURE: Variation analysis and Reporting Saskia Hiltemann
11:30 PRACTICAL: Variation analysis and Reporting Saskia Hiltemann / Andrew Stubbs
13:00 LUNCH
13:30 LECTURE / DEMO: Immunogenetics David van Zessen
14:00 LECTURE: RNAseq Tuxedo pipeline "end to end" Youri Hoogstrate
14:30 PRACTICAL: RNAseq Tuxedo pipeline "end to end" Youri Hoogstrate / Andrew Stubbs
15:30 BREAK
15:45 PRACTICAL: RNAseq Tuxedo pipeline "end to end" Youri Hoogstrate / Andrew Stubbs
16:30 LECTURE: wrap up for Day 1 Andrew Stubbs
16:45 END Day 1

6. Course Outline Time Description Presenter
09:00 LECTURE: Cancer Analysis in Galaxy Saskia Hiltemann
09:30 PRACTICAL: Cancer Analysis in Galaxy Saskia Hiltemann / Andrew Stubbs
11:00 BREAK
11:15 PRACTICAL: Cancer Analysis in Galaxy Saskia Hiltemann / Andrew Stubbs
13:00 LUNCH
13:30 LECTURE: Enhanced RNAseq Youri Hoogstrate
14:00 PRACTICAL: Enhanced RNAseq Youri Hoogstrate / Andrew Stubbs
15:30 BREAK
15:45 PRACTICAL: Enhanced RNAseq Youri Hoogstrate / Andrew Stubbs
16:30 LECTURE: Wrap Up from Two days Andrew Stubbs
16:45 END Day 2