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Improving RNA-Seq expression estimates by correcting for fragment bias

Roberts, Adam and Trapnell, Cole and Donaghey, Julie and Rinn, John L. and Pachter, Lior (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology, 12 (3). Art. No. R22. ISSN 1465-6906. PMCID PMC3129672. https://resolver.caltech.edu/CaltechAUTHORS:20170306-105110860

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Abstract

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://dx.doi.org/10.1186%2Fgb-2011-12-3-r22DOIArticle
http://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-3-r22PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129672/PubMed CentralArticle
Additional Information:© 2011 Roberts et al.; licensee BioMed Central Ltd. This article is published under license to BioMed Central Ltd. 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. Received: 4 December 2010. Accepted: 16 March 2011. Published: 16 March 2011. We thank Joshua Levin and Mitchell Guttman for their help with the NanoString experiment. Anat Caspi was instrumental in helping us obtain the SOLiD data. Adam Roberts was supported by an NSF graduate research fellowship. Authors' contributions: AR, CT and LP developed the bias correction approach. AR implemented the improvements to the Cufflinks software. JLR provided reagents and guidance. JD performed the NanoString experiment. AR performed the analysis. AR and LP wrote the paper. All authors read and approved the final manuscript.
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NSF Graduate Research FellowshipUNSPECIFIED
Issue or Number:3
PubMed Central ID:PMC3129672
Record Number:CaltechAUTHORS:20170306-105110860
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170306-105110860
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74779
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Mar 2017 20:42
Last Modified:03 Oct 2019 16:42

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