Hands-on: Analysis of Next Generation Sequencing Data with Genomatix

About this Class

Intended Audience: This day-long training course is intended for Users who want to apply Next Generation Sequencing methodologies for DNA-Seq, Methyl-Seq, small RNA-Seq, RNA-Seq and ChIP-Seq studies.  All analyses are done on the Genomatix Mining Station (GMS) and Genomatix Genome Analyzer (GGA)

1. Methodological background and Genomatix Mining Station (GMS):
   • Sequence statistics, mapping and mapping statistics
   • Read classification
   • Small variant detection
2. Methodological background and hands-on examples using Genomatix Genome Analyzer (GGA):
   • SNP analysis
   • Copy Number Variation (CNV) analysis
   • Methyl-Seq: Data Visualization
   • Small RNA-Seq and RNA-Seq: Expression Analysis
   • ChIP-Seq: Peak detection and analysis:
     • TF binding site analysis in ChIP peaks
     • De novo motif detection
     • Next-neighbor analysis and regulatory target prediction for ChIP regions
   • Meta analysis of different data sets