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Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.

Publication ,  Journal Article
Hsu, C-W; Shahan, R; Nolan, TM; Benfey, PN; Ohler, U
Published in: STAR protocols
December 2022

We describe a protocol to perform fast and non-arbitrary quality control of single-cell RNA sequencing (scRNA-seq) raw data using scKB and COPILOT. scKB is a wrapper script of kallisto and bustools for accelerated alignment and transcript count matrix generation, which runs significantly faster than the popular tool Cell Ranger. COPILOT then offers non-arbitrary background noise removal by comparing distributions of low-quality and high-quality cells. Together, this protocol streamlines the processing workflow and provides an easy entry for new scRNA-seq users. For complete details on the use and execution of this protocol, please refer to Shahan et al. (2022).

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Published In

STAR protocols

DOI

EISSN

2666-1667

ISSN

2666-1667

Publication Date

December 2022

Volume

3

Issue

4

Start / End Page

101729

Related Subject Headings

  • Software
  • Single-Cell Gene Expression Analysis
  • Single-Cell Analysis
  • Sequence Analysis, RNA
  • Quality Control
 

Citation

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MLA
NLM
Hsu, C.-W., Shahan, R., Nolan, T. M., Benfey, P. N., & Ohler, U. (2022). Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. STAR Protocols, 3(4), 101729. https://doi.org/10.1016/j.xpro.2022.101729
Hsu, Che-Wei, Rachel Shahan, Trevor M. Nolan, Philip N. Benfey, and Uwe Ohler. “Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.STAR Protocols 3, no. 4 (December 2022): 101729. https://doi.org/10.1016/j.xpro.2022.101729.
Hsu C-W, Shahan R, Nolan TM, Benfey PN, Ohler U. Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. STAR protocols. 2022 Dec;3(4):101729.
Hsu, Che-Wei, et al. “Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.STAR Protocols, vol. 3, no. 4, Dec. 2022, p. 101729. Epmc, doi:10.1016/j.xpro.2022.101729.
Hsu C-W, Shahan R, Nolan TM, Benfey PN, Ohler U. Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. STAR protocols. 2022 Dec;3(4):101729.
Journal cover image

Published In

STAR protocols

DOI

EISSN

2666-1667

ISSN

2666-1667

Publication Date

December 2022

Volume

3

Issue

4

Start / End Page

101729

Related Subject Headings

  • Software
  • Single-Cell Gene Expression Analysis
  • Single-Cell Analysis
  • Sequence Analysis, RNA
  • Quality Control