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

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Item Type:Article
Title:Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
Creators Name:Hsu, C.W., Shahan, R., Nolan, T.M., Benfey, P.N. and Ohler, U.
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, Single Cell, RNAseq, Systems Biology, Computer Sciences
Source:STAR Protocols
ISSN:2666-1667
Publisher:Elsevier
Volume:3
Number:4
Page Range:101729
Date:16 December 2022
Official Publication:https://doi.org/10.1016/j.xpro.2022.101729
PubMed:View item in PubMed

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