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

Journal Article (Journal Article)

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).

Full Text

Duke Authors

Cited Authors

  • Hsu, C-W; Shahan, R; Nolan, TM; Benfey, PN; Ohler, U

Published Date

  • December 2022

Published In

Volume / Issue

  • 3 / 4

Start / End Page

  • 101729 -

PubMed ID

  • 36181683

Pubmed Central ID

  • PMC9530667

Electronic International Standard Serial Number (EISSN)

  • 2666-1667

International Standard Serial Number (ISSN)

  • 2666-1667

Digital Object Identifier (DOI)

  • 10.1016/j.xpro.2022.101729


  • eng