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ShortFuse | Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

A package for using paired-end reads to find fusion transcripts without requiring unique mappings or additional single read sequencing. ShortFuse estimates fusion transcript abundances by considering physical coverage over the entire length of the proposed fusion. It employs several filters to minimize experimental artefacts and does not require that any single read sequence hit the point of fusion.

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ShortFuse forum

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ShortFuse classification

ShortFuse specifications

Unique identifier:
OMICS_01355
Interface:
Command line interface
Input data:
A transcriptome
Output format:
BEDPE
Programming languages:
C++, Python
Computer skills:
Advanced
Requirements:
Bowtie, GCC, NetworkX
Software type:
Package/Module
Restrictions to use:
None
Output data:
RefSeq IDs, names of the two genes involved in the fusion, score field
Operating system:
Unix/Linux
License:
BSD 2-clause “Simplified” License
Stability:
Stable
Maintained:
Yes

ShortFuse distribution

versioning

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ShortFuse support

Documentation

Credits

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Publications

Institution(s)

Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA

Funding source(s)

This tool was funded by the National Institutes of Health (grant numbers RO1-HG004962, 5U54HL108460, 1R21CA152613-01, CTSA-1U54RR025204) and the California Institute for Regenerative Medicine (grant number DR1-01430).

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.