Improving RNA-Seq expression estimates by correcting for fragment bias

The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based...

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Detalles Bibliográficos
Autores principales: Roberts, Adam, Trapnell, Cole, Donaghey, Julie, Rinn, John L, Pachter, Lior
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129672/
https://www.ncbi.nlm.nih.gov/pubmed/21410973
http://dx.doi.org/10.1186/gb-2011-12-3-r22
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author Roberts, Adam
Trapnell, Cole
Donaghey, Julie
Rinn, John L
Pachter, Lior
author_facet Roberts, Adam
Trapnell, Cole
Donaghey, Julie
Rinn, John L
Pachter, Lior
author_sort Roberts, Adam
collection PubMed
description The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies.
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spelling pubmed-31296722011-07-06 Improving RNA-Seq expression estimates by correcting for fragment bias Roberts, Adam Trapnell, Cole Donaghey, Julie Rinn, John L Pachter, Lior Genome Biol Method The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies. BioMed Central 2011 2011-03-16 /pmc/articles/PMC3129672/ /pubmed/21410973 http://dx.doi.org/10.1186/gb-2011-12-3-r22 Text en Copyright ©2011 Roberts 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
Roberts, Adam
Trapnell, Cole
Donaghey, Julie
Rinn, John L
Pachter, Lior
Improving RNA-Seq expression estimates by correcting for fragment bias
title Improving RNA-Seq expression estimates by correcting for fragment bias
title_full Improving RNA-Seq expression estimates by correcting for fragment bias
title_fullStr Improving RNA-Seq expression estimates by correcting for fragment bias
title_full_unstemmed Improving RNA-Seq expression estimates by correcting for fragment bias
title_short Improving RNA-Seq expression estimates by correcting for fragment bias
title_sort improving rna-seq expression estimates by correcting for fragment bias
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129672/
https://www.ncbi.nlm.nih.gov/pubmed/21410973
http://dx.doi.org/10.1186/gb-2011-12-3-r22
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