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Efficient and accurate detection of splice junctions from RNA-seq with Portcullis

Next-generation sequencing technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression, and alternative splicing. Key to this is the accurate identification of exon-exon junctions from RNA sequenced (RNA-seq) reads....

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Autores principales: Mapleson, Daniel, Venturini, Luca, Kaithakottil, Gemy, Swarbreck, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302956/
https://www.ncbi.nlm.nih.gov/pubmed/30418570
http://dx.doi.org/10.1093/gigascience/giy131
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author Mapleson, Daniel
Venturini, Luca
Kaithakottil, Gemy
Swarbreck, David
author_facet Mapleson, Daniel
Venturini, Luca
Kaithakottil, Gemy
Swarbreck, David
author_sort Mapleson, Daniel
collection PubMed
description Next-generation sequencing technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression, and alternative splicing. Key to this is the accurate identification of exon-exon junctions from RNA sequenced (RNA-seq) reads. A number of RNA-seq aligners capable of splitting reads across these splice junctions (SJs) have been developed; however, it has been shown that while they correctly identify most genuine SJs available in a given sample, they also often produce large numbers of incorrect SJs. Here, we describe the extent of this problem using popular RNA-seq mapping tools and present a new method, called Portcullis, to rapidly filter false SJs derived from spliced alignments. We show that Portcullis distinguishes between genuine and false-positive junctions to a high degree of accuracy across different species, samples, expression levels, error profiles, and read lengths. Portcullis is portable, efficient, and, to our knowledge, currently the only SJ prediction tool that reliably scales for use with large RNA-seq datasets and large, highly fragmented genomes, while delivering accurate SJs.
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spelling pubmed-63029562018-12-27 Efficient and accurate detection of splice junctions from RNA-seq with Portcullis Mapleson, Daniel Venturini, Luca Kaithakottil, Gemy Swarbreck, David Gigascience Tech Note Next-generation sequencing technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression, and alternative splicing. Key to this is the accurate identification of exon-exon junctions from RNA sequenced (RNA-seq) reads. A number of RNA-seq aligners capable of splitting reads across these splice junctions (SJs) have been developed; however, it has been shown that while they correctly identify most genuine SJs available in a given sample, they also often produce large numbers of incorrect SJs. Here, we describe the extent of this problem using popular RNA-seq mapping tools and present a new method, called Portcullis, to rapidly filter false SJs derived from spliced alignments. We show that Portcullis distinguishes between genuine and false-positive junctions to a high degree of accuracy across different species, samples, expression levels, error profiles, and read lengths. Portcullis is portable, efficient, and, to our knowledge, currently the only SJ prediction tool that reliably scales for use with large RNA-seq datasets and large, highly fragmented genomes, while delivering accurate SJs. Oxford University Press 2018-12-12 /pmc/articles/PMC6302956/ /pubmed/30418570 http://dx.doi.org/10.1093/gigascience/giy131 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Tech Note
Mapleson, Daniel
Venturini, Luca
Kaithakottil, Gemy
Swarbreck, David
Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
title Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
title_full Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
title_fullStr Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
title_full_unstemmed Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
title_short Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
title_sort efficient and accurate detection of splice junctions from rna-seq with portcullis
topic Tech Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302956/
https://www.ncbi.nlm.nih.gov/pubmed/30418570
http://dx.doi.org/10.1093/gigascience/giy131
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