Melsted, Páll and Ntranos, Vasilis and Pachter, Lior (2019) Barcode, UMI, Set format and BUStools. Bioinformatics, 35 (21). pp. 4472-4473. ISSN 1367-4803. https://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.
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| 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. | |||||||||
| Issue or Number: | 21 | |||||||||
| Record Number: | CaltechAUTHORS:20181128-093526289 | |||||||||
| Persistent URL: | https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526289 | |||||||||
| Official Citation: | Páll Melsted, Vasilis Ntranos, Lior Pachter, The barcode, UMI, set format and BUStools, Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4472–4473, 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: | 05 Nov 2019 15:50 |
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