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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....
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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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. |
format | Online Article Text |
id | pubmed-6302956 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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