SpliceMap protocols

SpliceMap specifications

Information


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

Versioning


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Documentation


Additional information


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

Publication for SpliceMap

SpliceMap IN pipeline

2014
PMCID: 4278777
PMID: 25565867
DOI: 10.2147/OTT.S72832

[…] adaptors were removed; 2) nucleotides with a quality score <20 were removed; 3) reads with more than 8% nitrogenous bases were removed. all subsequent analyses were based on clean reads.15, splicemap was used to detect splicing junctions and different types of as events, including exon skipping, mutually exclusive exons, intron retention, 5′as, and 3′as in cscc and atn tissues.16 […]

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

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