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

Che-Wei Hsu; Rachel Shahan; Trevor M Nolan; Philip N Benfey; Uwe Ohler

doi:10.1016/j.xpro.2022.101729

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

STAR Protoc. 2022 Dec 16;3(4):101729. doi: 10.1016/j.xpro.2022.101729. Epub 2022 Sep 30.

Authors

Che-Wei Hsu¹, Rachel Shahan², Trevor M Nolan², Philip N Benfey³, Uwe Ohler⁴

Affiliations

¹ 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.
² Department of Biology, Duke University, Durham, NC 27708, USA.
³ 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.
⁴ 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.

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).

Keywords: Bioinformatics; Computer sciences; RNAseq; Single cell; Systems biology.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

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

Abstract

Publication types

MeSH terms

Grants and funding