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Day 1 Pretoria

  • Project Introduction
  • Introduction to Using Galaxy
    • Basic examples introducing the Galaxy nterface and highlighting a wide range of Galaxy's functionality.
  • Next Generation Sequencing (NGS) Data Quality Control
    • Options for evaluating quality, trimming data, and tradeoffs involved.
  • RNA-Seq Analysis Example, Part I
    • Read Mapping and Transcript Prediction using the Tuxedo Suite of Tools


Day 2 Pretoria

  • RNA-Seq Analysis Example, Part II
    • Differential Expression Analysis with the Tuxedo Suite of Tools
  • RNA-Seq Analysis Example, Part III
    • RNA-Seq Analysis with a different set of tools
      Evaluate and discuss alternatives and selecting different approaches for different situations.

  • SNP and Variant Calling, Part I


Day 3 Pretoria

  • SNP and Variant Calling, Part II
  • ChIP-Seq Analysis


Day 4 Pretoria

  • Genome Assembly
  • Install your own Galaxy on Amazon Web Services


Day 5 Pretoria

  • Customizing Galaxy
  • Galaxy Tool Shed
  • Wrapping your own tools.