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Contents

• Overview
  • Before starting
  
  
• Requirements and Installation
  • Hardware
  • Operating system
  • Required softwares
  • Installation of ncPRO-seq
  
  
• How to use it ?
  • Configuration file
  • Web interface version
  • Command-line version
  
  
• How to browse the results ?
• How does-it work ?
  • Structure of the pipeline
  • Input pre-processing
  • Read mapping
  • Read annotation
  • Annotation analyses
  • Enrichment analysis
  
  
• Annotation files
  • Rfam annotation
  • RepeatMasker annotation
  • miRNA annotation
  • tRNA annotation
  • other annotations
  
  
• Installation of additional softwares
• Bibliography