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Annotation and Profiling of ncRNAs from smallRNA-seq



ncPRO-seq version 1.3.0

Chong-Jian Chen & Nicolas Servant

Date: Last updated : 31 May 2012

• Contents
• Overview
  • Before starting
  • About us
  
  
• Requirements and Installation
  • Hardware
  • Operating system
  • Required softwares
  • Installation of ncPRO-seq
  
  
• How to use it ?
  • Configuration file
  • Web interface version
    • Input data files
    • Alignment on a reference genome
    • Annotation Overview
    • Profiling of non-coding RNAs
    • Profiling of repetetive regions
    • User Custom gff files
    • Genome tracks visualisation
    • Search enriched regions
    • Run the analysis
  • Command-line version
  
  
• How to browse the results ?
• How does-it work ?
  • Structure of the pipeline
  • Input pre-processing
    • Read pre-processing
    • Alignment pre-processing
  • Reads mapping
  • Reads annotation
    • Reads with multiple mapping sites
    • Extension parameters
    • miRNAs read proportion
    • Reads annotation overview
    • Overview of repeat/Rfam
    • Read profiling in each family
    • Logo sequences
    • Read coverage in each annotation item
    • Track files
  • Enrichment analysis
  
  
• Annotation files
  • Rfam annotation
  • RepeatMasker annotation
  • miRNA annotation
  • tRNA annotation
  • Other annotations
  
  
• Installation of additional softwares
• FAQ
  • Enabling CGI using XAMPP
  • Working with a new genome
  
  
• Bibliography
• About this document ...