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SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

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...

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Detalles Bibliográficos
Autores principales: Huang, Songbo, Zhang, Jinbo, Li, Ruiqiang, Zhang, Wenqian, He, Zengquan, Lam, Tak-Wah, Peng, Zhiyu, Yiu, Siu-Ming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Research Foundation 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268599/
https://www.ncbi.nlm.nih.gov/pubmed/22303342
http://dx.doi.org/10.3389/fgene.2011.00046
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author Huang, Songbo
Zhang, Jinbo
Li, Ruiqiang
Zhang, Wenqian
He, Zengquan
Lam, Tak-Wah
Peng, Zhiyu
Yiu, Siu-Ming
author_facet Huang, Songbo
Zhang, Jinbo
Li, Ruiqiang
Zhang, Wenqian
He, Zengquan
Lam, Tak-Wah
Peng, Zhiyu
Yiu, Siu-Ming
author_sort Huang, Songbo
collection PubMed
description 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.
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spelling pubmed-32685992012-02-02 SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data Huang, Songbo Zhang, Jinbo Li, Ruiqiang Zhang, Wenqian He, Zengquan Lam, Tak-Wah Peng, Zhiyu Yiu, Siu-Ming Front Genet Genetics 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. Frontiers Research Foundation 2011-07-07 /pmc/articles/PMC3268599/ /pubmed/22303342 http://dx.doi.org/10.3389/fgene.2011.00046 Text en Copyright © 2011 Huang, Zhang, Li, Zhang, He, Lam, Peng and Yiu. http://www.frontiersin.org/licenseagreement This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and other Frontiers conditions are complied with.
spellingShingle Genetics
Huang, Songbo
Zhang, Jinbo
Li, Ruiqiang
Zhang, Wenqian
He, Zengquan
Lam, Tak-Wah
Peng, Zhiyu
Yiu, Siu-Ming
SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data
title SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data
title_full SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data
title_fullStr SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data
title_full_unstemmed SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data
title_short SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data
title_sort soapsplice: genome-wide ab initio detection of splice junctions from rna-seq data
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268599/
https://www.ncbi.nlm.nih.gov/pubmed/22303342
http://dx.doi.org/10.3389/fgene.2011.00046
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