Modeling non-uniformity in short-read rates in RNA-Seq data

After mapping, RNA-Seq data can be summarized by a sequence of read counts commonly modeled as Poisson variables with constant rates along each transcript, which actually fit data poorly. We suggest using variable rates for different positions, and propose two models to predict these rates based on...

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Detalles Bibliográficos
Autores principales: Li, Jun, Jiang, Hui, Wong, Wing Hung
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898062/
https://www.ncbi.nlm.nih.gov/pubmed/20459815
http://dx.doi.org/10.1186/gb-2010-11-5-r50
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author Li, Jun
Jiang, Hui
Wong, Wing Hung
author_facet Li, Jun
Jiang, Hui
Wong, Wing Hung
author_sort Li, Jun
collection PubMed
description After mapping, RNA-Seq data can be summarized by a sequence of read counts commonly modeled as Poisson variables with constant rates along each transcript, which actually fit data poorly. We suggest using variable rates for different positions, and propose two models to predict these rates based on local sequences. These models explain more than 50% of the variations and can lead to improved estimates of gene and isoform expressions for both Illumina and Applied Biosystems data.
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spelling pubmed-28980622010-07-07 Modeling non-uniformity in short-read rates in RNA-Seq data Li, Jun Jiang, Hui Wong, Wing Hung Genome Biol Method After mapping, RNA-Seq data can be summarized by a sequence of read counts commonly modeled as Poisson variables with constant rates along each transcript, which actually fit data poorly. We suggest using variable rates for different positions, and propose two models to predict these rates based on local sequences. These models explain more than 50% of the variations and can lead to improved estimates of gene and isoform expressions for both Illumina and Applied Biosystems data. BioMed Central 2010 2010-05-11 /pmc/articles/PMC2898062/ /pubmed/20459815 http://dx.doi.org/10.1186/gb-2010-11-5-r50 Text en Copyright ©2010 Li 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
Li, Jun
Jiang, Hui
Wong, Wing Hung
Modeling non-uniformity in short-read rates in RNA-Seq data
title Modeling non-uniformity in short-read rates in RNA-Seq data
title_full Modeling non-uniformity in short-read rates in RNA-Seq data
title_fullStr Modeling non-uniformity in short-read rates in RNA-Seq data
title_full_unstemmed Modeling non-uniformity in short-read rates in RNA-Seq data
title_short Modeling non-uniformity in short-read rates in RNA-Seq data
title_sort modeling non-uniformity in short-read rates in rna-seq data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898062/
https://www.ncbi.nlm.nih.gov/pubmed/20459815
http://dx.doi.org/10.1186/gb-2010-11-5-r50
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AT jianghui modelingnonuniformityinshortreadratesinrnaseqdata
AT wongwinghung modelingnonuniformityinshortreadratesinrnaseqdata

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