1. Galaxy course EMC TraIT Nov 2014_Jenster
Data analysis and integration
How to get from a pile of unprocessed data to knowledge:
The user’s perspective
Guido Jenster, Ph.D.
Professor of Experimental Urological Oncology
Department of Urology
Erasmus MC

2. Experimental Research
Prostate Cancer Molecular Medicine
Clinical Research
Biobanking
Experimental Research
Imaging
DATA
QUERY
VIEWING
DATA INTEGRATION
DATA PROCESSING
NEW KNOWLEDGE
DATA STORAGE
DATA GENERATION

3. Prostate Cancer Molecular Medicine
What do we want?
Use case:
Identify novel fusion genes from DNA and RNA sequencing data
PUSH TO
START

4. Copy Number Abberations
DNAseq Data Analysis
SNVs / InDels
Copy Number Abberations
TF Binding
B-Allele Frequency
DNAseq data
Chromatin Interactions
Structural Variations
Methylation
Active Chromatin
Identify
Integration Sites
Read
Barcode

5. Differential expression
RNAseq Data Analysis
Differential expression
SNVs / InDels
RNAseq data
Alternative splicing &
Promoters
Read-Through & Fusion Transcripts
Novel Transcripts

6. TraIT Galaxy

7. Work Flows

8. The TraIT mansion requires good support
WP4
Phenotype
Database
BMIA
Data storage + CPU power
TTP
SurfConext
Catalogue
Open
Clinica
Chipster
XNAT
tEPIS
Logis
Workflow
Galaxy
Keosys
coLIMS
tranSMART
TOP
desk
Alfresco
Website
Wiki
Jira