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Quantifying uniformity of mapped reads

Hower, Valerie and Starfield, Richard and Roberts, Adam and Pachter, Lior (2012) Quantifying uniformity of mapped reads. Bioinformatics, 28 (20). pp. 2680-2682. ISSN 1367-4803. PMCID PMC3467739. doi:10.1093/bioinformatics/bts451. https://resolver.caltech.edu/CaltechAUTHORS:20170303-164056261

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Abstract

We describe a tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. Our statistic directly measures the uniformity of both read position and fragment length, and we explain how to compute a P-value that can be used to quantify biases arising from experimental protocols and mapping procedures. Our method is useful for comparing different protocols in experiments such as RNA-Seq. Availability and implementation: We provide a freely available and open source python script that can be used to analyze raw read data or reads mapped to transcripts in BAM format at http://www.math.miami.edu/~vhower/ReadSpy.html


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/bioinformatics/bts451DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467739/PubMed CentralArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© The Author 2012. Published by Oxford University Press on behalf of The Society for Financial Studies. Received: 20 September 2012. Revision Received: 04 July 2012. Accepted: 05 July 2012. V.H. was funded in part by NSF fellowship DMS-0902723. A.R and L.P. were funded in part by NIH R01 HG006129. A.R. was also funded in part by an NSF graduate research fellowship. Conflict of Interest: none declared.
Funders:
Funding AgencyGrant Number
NSF Graduate Research FellowshipDMS-0902723
NIHR01 HG006129
Issue or Number:20
PubMed Central ID:PMC3467739
DOI:10.1093/bioinformatics/bts451
Record Number:CaltechAUTHORS:20170303-164056261
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170303-164056261
Official Citation:Valerie Hower, Richard Starfield, Adam Roberts, Lior Pachter; Quantifying uniformity of mapped reads. Bioinformatics 2012; 28 (20): 2680-2682. doi: 10.1093/bioinformatics/bts451
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74748
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Mar 2017 16:51
Last Modified:11 Nov 2021 05:29

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