Work

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

Year: 2022

Type: article

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).

Source: STAR Protocols

DOI: 10.1016/j.xpro.2022.101729

Authors: Che-Wei Hsu, Rachel Shahan, Trevor M. Nolan, Philip N. Benfey, Uwe Ohler

Institutions: Max Delbrück Center, Humboldt-Universität zu Berlin, Duke University, Howard Hughes Medical Institute

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $1,500