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

Journal: STAR protocols
Published Date: Sep 30, 2022

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).

Authors

  • Che-Wei Hsu
    Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany.
  • Rachel Shahan
    Department of Biology, Duke University, Durham, NC 27708, USA.
  • Trevor M Nolan
    Department of Biology, Duke University, Durham, NC 27708, USA.
  • Philip N Benfey
    Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA. Electronic address: philip.benfey@duke.edu.
  • Uwe Ohler
    Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany. Electronic address: uwe.ohler@mdc-berlin.de.

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