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

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...

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Detalles Bibliográficos
Autores principales: Hsu, Che-Wei, Shahan, Rachel, Nolan, Trevor M., Benfey, Philip N., Ohler, Uwe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9530667/
https://www.ncbi.nlm.nih.gov/pubmed/36181683
http://dx.doi.org/10.1016/j.xpro.2022.101729
Descripción
Sumario: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).

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