Published November 1, 2019
| Submitted + Published + Supplemental Material
Journal Article
Open
Barcode, UMI, Set format and BUStools
- Creators
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Melsted, Páll
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Ntranos, Vasilis
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Pachter, Lior
Chicago
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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.
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.Attached Files
Published - btz279.pdf
Submitted - 472571.full.pdf
Supplemental Material - btz279_supplmentary.pdf
Files
472571.full.pdf
Additional details
- Eprint ID
- 91273
- Resolver ID
- CaltechAUTHORS:20181128-093526289
- Created
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2018-11-28Created from EPrint's datestamp field
- Updated
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2023-06-01Created from EPrint's last_modified field