Article: SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-seq data

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TitleSOAPsplice: genome-wide ab initio detection of splice junctions from RNA-seq data
AuthorsHuang, S
Zhang, J
Li, R
Zhang, W
He, Z
Lam, TW
Peng, Z
Yiu, SM
KeywordsRNA-Seq
Splice junction
Spliced alignment
Issue Date2011
PublisherFrontiers Media SA. The Journal's web site is located at http://www.frontiersin.org/Genomic_Assay_Technology
CitationFrontiers in Genomic Assay Technology, 2011, v. 2, article no. 46 [How to Cite?]
DOI: http://dx.doi.org/10.3389/fgene.2011.00046
AbstractRNA-Seq, a method using next generation sequencing technologies to sequence the transcriptome, facilitates genome-wide analysis of splice junction sites. In this paper, we introduce SOAPsplice, a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. SOAPsplice uses a novel two-step approach consisting of first identifying as many reasonable splice junction candidates as possible, and then, filtering the false positives with two effective filtering strategies. In both simulated and real datasets, SOAPsplice is able to detect many reliable splice junctions with low false positive rate. The improvement gained by SOAPsplice, when compared to other existing tools, becomes more obvious when the depth of sequencing is low. SOAPsplice is freely available at http://soap.genomics.org.cn/soapsplice.html.
DescriptionOpen Access Journal
DOIhttp://dx.doi.org/10.3389/fgene.2011.00046
DC Field
Value
dc.contributor.authorHuang, S
dc.contributor.authorZhang, J
dc.contributor.authorLi, R
dc.contributor.authorZhang, W
dc.contributor.authorHe, Z
dc.contributor.authorLam, TW
dc.contributor.authorPeng, Z
dc.contributor.authorYiu, SM
dc.date.accessioned2012-09-20T08:24:30Z
dc.date.available2012-09-20T08:24:30Z
dc.date.issued2011
dc.description.abstractRNA-Seq, a method using next generation sequencing technologies to sequence the transcriptome, facilitates genome-wide analysis of splice junction sites. In this paper, we introduce SOAPsplice, a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. SOAPsplice uses a novel two-step approach consisting of first identifying as many reasonable splice junction candidates as possible, and then, filtering the false positives with two effective filtering strategies. In both simulated and real datasets, SOAPsplice is able to detect many reliable splice junctions with low false positive rate. The improvement gained by SOAPsplice, when compared to other existing tools, becomes more obvious when the depth of sequencing is low. SOAPsplice is freely available at http://soap.genomics.org.cn/soapsplice.html.
dc.description.naturelink_to_OA_fulltext
dc.descriptionOpen Access Journal
dc.identifier.citationFrontiers in Genomic Assay Technology, 2011, v. 2, article no. 46 [How to Cite?]
DOI: http://dx.doi.org/10.3389/fgene.2011.00046
dc.identifier.citeulike10360369
dc.identifier.doihttp://dx.doi.org/10.3389/fgene.2011.00046
dc.identifier.hkuros208233
dc.identifier.urihttp://hdl.handle.net/10722/165846
dc.identifier.volume2, article no. 46
dc.languageeng
dc.publisherFrontiers Media SA. The Journal's web site is located at http://www.frontiersin.org/Genomic_Assay_Technology
dc.publisher.placeSwitzerland
dc.relation.ispartofFrontiers in Genomic Assay Technology
dc.subjectRNA-Seq
dc.subjectSplice junction
dc.subjectSpliced alignment
dc.titleSOAPsplice: genome-wide ab initio detection of splice junctions from RNA-seq data
dc.typeArticle