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

TitleSOAPsplice: genome-wide ab initio detection of splice junctions from RNA-seq data
Authors
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
Citation
Frontiers in Genomic Assay Technology, 2011, v. 2, article no. 46 How to Cite?
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.
DescriptionOpen Access Journal
Persistent Identifierhttp://hdl.handle.net/10722/165846

 

DC FieldValueLanguage
dc.contributor.authorHuang, Sen_US
dc.contributor.authorZhang, Jen_US
dc.contributor.authorLi, Ren_US
dc.contributor.authorZhang, Wen_US
dc.contributor.authorHe, Zen_US
dc.contributor.authorLam, TWen_US
dc.contributor.authorPeng, Zen_US
dc.contributor.authorYiu, SMen_US
dc.date.accessioned2012-09-20T08:24:30Z-
dc.date.available2012-09-20T08:24:30Z-
dc.date.issued2011en_US
dc.identifier.citationFrontiers in Genomic Assay Technology, 2011, v. 2, article no. 46en_US
dc.identifier.urihttp://hdl.handle.net/10722/165846-
dc.descriptionOpen Access Journal-
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.languageengen_US
dc.publisherFrontiers Media SA. The Journal's web site is located at http://www.frontiersin.org/Genomic_Assay_Technology-
dc.relation.ispartofFrontiers in Genomic Assay Technologyen_US
dc.subjectRNA-Seq-
dc.subjectSplice junction-
dc.subjectSpliced alignment-
dc.titleSOAPsplice: genome-wide ab initio detection of splice junctions from RNA-seq dataen_US
dc.typeArticleen_US
dc.identifier.emailLam, TW: hresltk@hkucc.hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.authorityLam, TW=rp00135en_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.3389/fgene.2011.00046-
dc.identifier.hkuros208233en_US
dc.identifier.volume2, article no. 46en_US
dc.publisher.placeSwitzerland-
dc.identifier.citeulike10360369-

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