RNA Seq course

Contents:

• Introduction
• Experiment Design
  • Exercise
• A brief introduction to linux shell
  • Navigating in the file system
  • Some more commands
  • Redirect and pipe
  • Exercises
• RNA Seq raw data
  • MD5Sum
  • The fastq file format
  • Quality control
  • Quality trimming
  • Exercise
• Gapped Alignment
  • Hands-on exercise
  • Mapping
  • Processing with SAMTOOLS
  • Data visualization
  • Exercise
• Measuring expression levels from RNA Seq data
  • Expression values / Transcript abundance
  • Calculating expression values
  • Exercise
• De novo RNA Seq assembly
  • Exercise