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Alt Event Finder - Yunlong Liu Lab

Alt Event Finder: A tool for extracting alternative splicing events from RNA-seq data
 
Introduction
Alt Event Finder is a software tool for deriving data-driven alternative splicing (AS) events from RNA-seq data. It analyses the transcripts built by Cufflinks or Scripture and outputs AS event annotations which is compatible with MISO. Alt Event Finder can be used for annotating novel AS events from a well-annotated species such as human. It can also be used for species of which known AS event annotation is not available. The current release (v0.1) supports skipped exon events only.
 
Releases
Alt Event Finder v0.1 (AltEventFinder_v0.1.tar.gz), January 22, 2013 release
 
Requirement
  1. Perl
  2. R
  3. DBD SQLite
 
Installation
  1. Extract the package where you want to install Alt Event Finder:
    tar xzvf AltEventFinder.tar.gz
  2. Add the Alt Event Finder directory to the PATH environment variable, as follows (for bash-shell like systems):
    export PATH=~/AltEventFinder/:$PATH
 
Workflow
  1. Map RNA-seq reads to genome with short read aligners (Tophat, our customized pipeline base on bfast, etc).
  2. Build transcripts with transcript assembly software (Cufflinks or Scripture). If Cufflinks is used, the output will be in GTF format; if Scripture is used, the output will be in BED format (with a suffix “.segments”).
  3. Pass the transcript annotations to AS Event Finder and derive AS event annotations in GFF3 format.
  4. Apply MISO analysis with AS event annotations.
 
Usage
  1. Download test files:
    CufflinksFormat.gtf.tar.gz
    ScriptureFormat.segments.tar.gz
  2. Extract the test files:
    tar xzvf CufflinksFormat.gtf.tar.gz
    tar xzvf ScriptureFormat.segments.tar.gz
  3. For CufflinksFormat.gtf, run the following command:
    alt_event_finder --cufflinks CufflinksFormat.gtf CufflinksFormat
    For ScriptureFormat.segments, run the following command:
    alt_event_finder --scripture ScriptureFormat.segments ScriptureFormat
  4. If the program runned successfully, a directory named CufflinksFormat or ScriptureFormat can be found. Inside the directory there will be a file named SE.gff3, and that is the skipped exon (SE) annotations. The current version supports SE events only, support for other types of events is still under development.
 
Publication
Zhou A, Breese MR, Hao Y, Edenberg HJ, Li L, Skaar TC, Liu Y: Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data. BMC genomics 2012, 13 Suppl 8:S10.