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ncPRO-seq
Annotation and Profiling of ncRNAs from smallRNA-seq
Chong-Jian Chen & Nicolas Servant
Date:
Last updated : 26 January 2012
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
Input data files
Alignment on a reference genome
Annotation of non-coding RNAs
Annotation 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
Read mapping
Read annotation
Annotation analyses
Reads with multiple mapping sites
Extension parameters
MiRNA read proportion
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
Bibliography
About this document ...
Chongjian Chen 2012-01-26
