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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 FieldValue
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
 
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<contributor.author>Zhang, J</contributor.author>
<contributor.author>Li, R</contributor.author>
<contributor.author>Zhang, W</contributor.author>
<contributor.author>He, Z</contributor.author>
<contributor.author>Lam, TW</contributor.author>
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<description.abstract>RNA-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.</description.abstract>
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