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Alt Event Finder | A tool for extracting alternative splicing events from RNA-seq data

Allows users to generate splicing event annotations from RNA-seq data. Alt Event Finder is a flexible standalone software, based on a data-driven approach, that started from reconstructed map of transcripts and isoforms from RNA-seq experiments to determine the potential alternative events and identify unknown cassette exon. Nevertheless, the power of the program depends on the sequencing depth.

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Alt Event Finder forum

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Alt Event Finder classification

Alt Event Finder specifications

Unique identifier:
OMICS_01941
Interface:
Command line interface
Input format:
GTF,BED
Output format:
GFF3
Programming languages:
Perl, R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Software type:
Application/Script
Restrictions to use:
None
Output data:
A list of alternative splicing events.
Operating system:
Unix/Linux
Database management system:
SQLite
Version:
0.1
Requirements:
DBD SQLite

Alt Event Finder distribution

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Alt Event Finder support

Maintainer

  • Yunlong Liu <>

Credits

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Publications

Institution(s)

Bioinformatics Program, School of Informatics, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA

Funding source(s)

Supported by supported by the grants from the National Institutes of Health AA017941, CA113001, GM085121, and GM088076.

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