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Streaming fragment assignment for real-time analysis of sequencing experiments

Roberts, Adam and Pachter, Lior (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods, 10 (1). pp. 71-73. ISSN 1548-7091. PMCID PMC3880119. doi:10.1038/nmeth.2251. https://resolver.caltech.edu/CaltechAUTHORS:20170303-163300268

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Abstract

We present eXpress, a software package for efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. We demonstrate its use on RNA-seq data and show that eXpress achieves greater efficiency than other quantification methods.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/nmeth.2251DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880119/PubMed CentralArticle
http://rdcu.be/pMBFPublisherFree ReadCube access
http://www.ncbi.nlm.nih.gov/sra?term=SRX026669OrganizationSequence Read Archive
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2012 Macmillan Publishers Limited. Received 30 April 2012. Accepted 26 October 2012. Published online 18 November 2012. Corrected online 04 December 2012. This work was supported by US National Institutes of Health grant R01HG006129. A.R. was supported in part by a National Science Foundation graduate research fellowship. We thank H. Pimentel for developing Map2GTF for converting genome mappings to transcriptome mappings and incorporating it into TopHat to help with our analysis. Author Contributions: A.R. and L.P. developed the mathematics and statistics and designed the algorithms. A.R. implemented the method in eXpress. A.R. and L.P. tested the software and performed the analysis. A.R. and L.P. wrote the manuscript. The authors declare no competing financial interests.
Errata:Corrected online 04 December 2012 In the HTML version of this article initially published online, errors in mathematical terms were present in the Online Methods section. The errors have been corrected in the HTML version.
Funders:
Funding AgencyGrant Number
NIHR01 HG006129
NSF Graduate Research FellowshipUNSPECIFIED
Issue or Number:1
PubMed Central ID:PMC3880119
DOI:10.1038/nmeth.2251
Record Number:CaltechAUTHORS:20170303-163300268
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170303-163300268
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74746
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Mar 2017 17:16
Last Modified:11 Nov 2021 05:29

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