Global and unbiased detection of splice junctions from RNA-seq data

We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separ...

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Detalles Bibliográficos
Autores principales: Ameur, Adam, Wetterbom, Anna, Feuk, Lars, Gyllensten, Ulf
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864574/
https://www.ncbi.nlm.nih.gov/pubmed/20236510
http://dx.doi.org/10.1186/gb-2010-11-3-r34
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author Ameur, Adam
Wetterbom, Anna
Feuk, Lars
Gyllensten, Ulf
author_facet Ameur, Adam
Wetterbom, Anna
Feuk, Lars
Gyllensten, Ulf
author_sort Ameur, Adam
collection PubMed
description We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by ≤100 kb, and 74% connected two exons of the same RefSeq gene. Our method also reports genomic rearrangements such as insertions and deletions.
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spelling pubmed-28645742010-05-05 Global and unbiased detection of splice junctions from RNA-seq data Ameur, Adam Wetterbom, Anna Feuk, Lars Gyllensten, Ulf Genome Biol Method We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by ≤100 kb, and 74% connected two exons of the same RefSeq gene. Our method also reports genomic rearrangements such as insertions and deletions. BioMed Central 2010 2010-03-17 /pmc/articles/PMC2864574/ /pubmed/20236510 http://dx.doi.org/10.1186/gb-2010-11-3-r34 Text en Copyright ©2010 Ameur et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Ameur, Adam
Wetterbom, Anna
Feuk, Lars
Gyllensten, Ulf
Global and unbiased detection of splice junctions from RNA-seq data
title Global and unbiased detection of splice junctions from RNA-seq data
title_full Global and unbiased detection of splice junctions from RNA-seq data
title_fullStr Global and unbiased detection of splice junctions from RNA-seq data
title_full_unstemmed Global and unbiased detection of splice junctions from RNA-seq data
title_short Global and unbiased detection of splice junctions from RNA-seq data
title_sort global and unbiased detection of splice junctions from rna-seq data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864574/
https://www.ncbi.nlm.nih.gov/pubmed/20236510
http://dx.doi.org/10.1186/gb-2010-11-3-r34
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AT feuklars globalandunbiaseddetectionofsplicejunctionsfromrnaseqdata
AT gyllenstenulf globalandunbiaseddetectionofsplicejunctionsfromrnaseqdata

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