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Barcode, UMI, Set format and BUStools

Melsted, Páll and Ntranos, Vasilis and Pachter, Lior (2019) Barcode, UMI, Set format and BUStools. Bioinformatics . ISSN 1367-4803. (In Press) http://resolver.caltech.edu/CaltechAUTHORS:20181128-093526289

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Abstract

We introduce the Barcode-UMI-Set format (BUS) for representing pseudoalignments of reads from single-cell RNA-seq experiments. The format can be used with all single-cell RNA-seq technologies, and we show that BUS files can be efficiently generated. BUStools is a suite of tools for working with BUS files and facilitates rapid quantification and analysis of single-cell RNA-seq data. The BUS format therefore makes possible the development of modular, technology-specific, and robust workflows for single-cell RNA-seq analysis.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/bioinformatics/btz279DOIArticle
https://doi.org/10.1101/472571DOIDiscussion Paper
ORCID:
AuthorORCID
Melsted, Páll0000-0002-8418-6724
Ntranos, Vasilis0000-0002-2477-0670
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2019 The Author(s). Published by Oxford University Press. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Received: 26 November 2018; Revision Received: 15 February 2019; Accepted: 11 April 2019; Published: 09 May 2019. We thank Fan Gao for helping with the benchmarking of 'kallisto bus' and BUStools. Valentine Svensson provided valuable suggestions, and we relied on his compilation of scRNA-seq read encodings (Svensson et al. 2017). Jase Gehring, Lynn Yi and Tina Wang provided valuable feedback on an initial kallisto-based scRNA-seq workflow, which motivated the development of the BUS format.
Record Number:CaltechAUTHORS:20181128-093526289
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20181128-093526289
Official Citation:Páll Melsted, Vasilis Ntranos, Lior Pachter, The Barcode, UMI, Set format and BUStools, Bioinformatics, , btz279, https://doi.org/10.1093/bioinformatics/btz279
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91273
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:28 Nov 2018 18:06
Last Modified:13 May 2019 16:42

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