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

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2022-12

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Abstract

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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Journal article

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

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https://hdl.handle.net/10161/26565

Published Version (Please cite this version)

10.1016/j.xpro.2022.101729

Publication Info

Hsu, Che-Wei, Rachel Shahan, Trevor M Nolan, Philip N Benfey and Uwe Ohler (2022). Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. STAR protocols, 3(4). p. 101729. 10.1016/j.xpro.2022.101729 Retrieved from https://hdl.handle.net/10161/26565.

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Shahan

Rachel Shahan

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Benfey Lab

Education

  • Ph.D. Cell Biology and Molecular Genetics. University of Maryland. College Park, Maryland.
  • B.S. Biology. Virginia Tech. Blacksburg, Virginia. 

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