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Published November 1, 2019 | Submitted + Published + Supplemental Material
Journal Article Open

Barcode, UMI, Set format and BUStools

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

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Additional details

Created:
August 19, 2023
Modified:
October 20, 2023