Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference

We introduce Salmon, a method for quantifying transcript abundance from RNA-seq reads that is accurate and fast. Salmon is the first transcriptome-wide quantifier to correct for fragment GC content bias, which we demonstrate substantially improves the accuracy of abundance estimates and the reliabil...

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Detalles Bibliográficos
Autores principales: Patro, Rob, Duggal, Geet, Love, Michael I, Irizarry, Rafael A, Kingsford, Carl
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2017
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5600148/
https://www.ncbi.nlm.nih.gov/pubmed/28263959
http://dx.doi.org/10.1038/nmeth.4197
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author Patro, Rob
Duggal, Geet
Love, Michael I
Irizarry, Rafael A
Kingsford, Carl
author_facet Patro, Rob
Duggal, Geet
Love, Michael I
Irizarry, Rafael A
Kingsford, Carl
author_sort Patro, Rob
collection PubMed
description We introduce Salmon, a method for quantifying transcript abundance from RNA-seq reads that is accurate and fast. Salmon is the first transcriptome-wide quantifier to correct for fragment GC content bias, which we demonstrate substantially improves the accuracy of abundance estimates and the reliability of subsequent differential expression analysis. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure.
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spelling pubmed-56001482017-09-19 Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference Patro, Rob Duggal, Geet Love, Michael I Irizarry, Rafael A Kingsford, Carl Nat Methods Article We introduce Salmon, a method for quantifying transcript abundance from RNA-seq reads that is accurate and fast. Salmon is the first transcriptome-wide quantifier to correct for fragment GC content bias, which we demonstrate substantially improves the accuracy of abundance estimates and the reliability of subsequent differential expression analysis. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure. 2017-03-06 2017-04 /pmc/articles/PMC5600148/ /pubmed/28263959 http://dx.doi.org/10.1038/nmeth.4197 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Patro, Rob
Duggal, Geet
Love, Michael I
Irizarry, Rafael A
Kingsford, Carl
Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference
title Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference
title_full Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference
title_fullStr Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference
title_full_unstemmed Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference
title_short Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference
title_sort salmon: fast and bias-aware quantification of transcript expression using dual-phase inference
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5600148/
https://www.ncbi.nlm.nih.gov/pubmed/28263959
http://dx.doi.org/10.1038/nmeth.4197
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