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Updating RNA-Seq analyses after re-annotation

Roberts, Adam and Schaeffer, Lorian and Pachter, Lior (2013) Updating RNA-Seq analyses after re-annotation. Bioinformatics, 29 (13). pp. 1631-1637. ISSN 1367-4803. PMCID PMC3694665. doi:10.1093/bioinformatics/btt197. https://resolver.caltech.edu/CaltechAUTHORS:20170303-154642805

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Abstract

The estimation of isoform abundances from RNA-Seq data requires a time-intensive step of mapping reads to either an assembled or previously annotated transcriptome, followed by an optimization procedure for deconvolution of multi-mapping reads. These procedures are essential for downstream analysis such as differential expression. In cases where it is desirable to adjust the underlying annotation, for example, on the discovery of novel isoforms or errors in existing annotations, current pipelines must be rerun from scratch. This makes it difficult to update abundance estimates after re-annotation, or to explore the effect of changes in the transcriptome on analyses. We present a novel efficient algorithm for updating abundance estimates from RNA-Seq experiments on re-annotation that does not require re-analysis of the entire dataset. Our approach is based on a fast partitioning algorithm for identifying transcripts whose abundances may depend on the added or deleted isoforms, and on a fast follow-up approach to re-estimating abundances for all transcripts. We demonstrate the effectiveness of our methods by showing how to synchronize RNA-Seq abundance estimates with the daily RefSeq incremental updates. Thus, we provide a practical approach to maintaining relevant databases of RNA-Seq derived abundance estimates even as annotations are being constantly revised.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/bioinformatics/btt197DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694665/PubMed CentralArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© The Author 2013. Published by Oxford University Press. Received and revised on April 11, 2013; accepted on April 21, 2013. We thank Isabelle Stanton for her advice on graph partitioning. Funding: AR was partly funded by an NSF graduate fellowship. AR and LP were partially funded by NIH R01 HG006129. Conflict of Interest: none declared. Availability and implementation: Our methods are implemented in software called ReXpress and are freely available, together with source code, at http://bio.math.berkeley.edu/ReXpress/.
Funders:
Funding AgencyGrant Number
NSF Graduate Research FellowshipUNSPECIFIED
NIHR01 HG006129
Issue or Number:13
PubMed Central ID:PMC3694665
DOI:10.1093/bioinformatics/btt197
Record Number:CaltechAUTHORS:20170303-154642805
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170303-154642805
Official Citation:Adam Roberts, Lorian Schaeffer, Lior Pachter; Updating RNA-Seq analyses after re-annotation. Bioinformatics 2013; 29 (13): 1631-1637. doi: 10.1093/bioinformatics/btt197
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74738
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:04 Mar 2017 00:16
Last Modified:11 Nov 2021 05:29

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