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SpliceMap | Detection of splice junctions from paired-end RNA-seq data

Detects splice junctions from RNA-seq data. SpliceMap does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads and can exploit paired-read information to improve mapping accuracy. Workflow of standard SpliceMap and outline of junction search based on half-read mapping, it consists of four steps: half-read mapping, seeding selection, junction search and paired-end filtering.

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SpliceMap forum

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SpliceMap classification

SpliceMap specifications

Unique identifier:
OMICS_01252
Interface:
Command line interface
Input format:
SAM, BED, WIG
Computer skills:
Advanced
Maintained:
Yes
Software type:
Application/Script
Restrictions to use:
None
Operating system:
Unix/Linux
Stability:
Stable

SpliceMap distribution

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No versioning.

SpliceMap support

Documentation

Additional information

http://web.stanford.edu/group/wonglab/SpliceMap/tutorial.html

Credits

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Publications

Institution(s)

Department of Statistics, Stanford University, Stanford, CA, USA; Stanford Genome Technology Center, Palo Alto, CA, USA; Department of Internal Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA

Funding source(s)

National Institutes of Health (1R01HG004634); Junior faculty grant from the Edward
Mallinckrodt Jr. Foundation

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