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EMBL Advanced Course

Next Generation Sequencing Data Analysis

EMBL Heidelberg, Germany Tuesday 16 October - Thursday 18 October 2012 Application closed
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Final Programme

 
Day 1 - Tuesday, 16 October 2012
12:00 - 17:00

Talk: Vladimir Benes, GeneCore at EMBL Heidelberg, on NGS library preparation

  • Introduction to Genomatix Mining Station (GMS) - methodological background
  • GMS demonstration: mapping, SNP detection, read classification
  • Hands-on example using the GGA: SNP analysis and evaluation
 
 
Day 2 - Wednesday, 17 October 2012
09:00 - 12:00

Talk: Jonathon Blake, GeneCore at EMBL Heidelberg, on RNA sequencing

Introduction to Genomatix Genome Analyzer (GGA) - RNA-Seq analysis

Hands-on examples using the GGA (expression analysis):

  • Differential expression
  • Assessment of related biology
  • Data visualization
12:00 - 13:00 Lunch
13:00 - 17:00 Genomatix Genome Analyzer (GGA) - ChIP-Seq analysis overview

Hands-on examples using the GGA (ChIP-Seq analysis):

  • Expression analysis
  • Data visualization
  • Peak detection and classification
  • TF binding site analysis in ChIP peaks
  • De novo definition of common sequence motifs from ChIP data
  • Next-neighbor analysis and regulatory target prediction for ChIP regions
  • Meta analysis of different data sets  
 
 
Day 3 - Thursday, 18 October 2012
09:00 - 12:00 This day is reserved for the analysis of your own data. In order for you to be able to use your data in the course, please make sure of the following:
Firstly, that the format and content of your data is supported by the Genomatix system. Please consult the link you will receive after selection for supported data formats and source organisms. Secondly, if you have data it must reach us one week before the course at the latest; this time is needed for mapping (if you have sequence data) and to verify data compatibility (if you have mapped data). You will be given a detailed description how to upload your data in your course confirmation email.
09:00 Talk: George Reid, IMB Mainz, on methylation studies
12:00 - 13:00 Lunch