Contents

• Overview
• Requirements
  • Recommendations
  
  
• Preparations
  • Alignment
  • Sorting
  
  
• Quick Start
• Dataset Organization
  • Example data
  
  
• Processing of aligned RNA-Seq data
  • Memory Usage
  
  
• Visualization
  • Reading the QC data into R
  • Generating all default plots
  • Plotting by sample, lane, or group
  • Description of Individual Plots
  
  
• Identifying Problems
  • Example 1: Sequencer Hiccup
  • Example 2: Badly Degraded RNA
  
  
• Secondary Utilities
  • Generating a flattened annotation file
  • Merging Count Data
  • Generating genome browser tracks
  • Importing data into other tools
  
  
• Bibliography
• Session Information
• Legal