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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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
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author Hsu, Che-Wei
Shahan, Rachel
Nolan, Trevor M.
Benfey, Philip N.
Ohler, Uwe
author_facet Hsu, Che-Wei
Shahan, Rachel
Nolan, Trevor M.
Benfey, Philip N.
Ohler, Uwe
author_sort Hsu, Che-Wei
collection PubMed
description 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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spelling pubmed-95306672022-10-05 Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT Hsu, Che-Wei Shahan, Rachel Nolan, Trevor M. Benfey, Philip N. Ohler, Uwe STAR Protoc Protocol 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). Elsevier 2022-09-30 /pmc/articles/PMC9530667/ /pubmed/36181683 http://dx.doi.org/10.1016/j.xpro.2022.101729 Text en © 2022. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Hsu, Che-Wei
Shahan, Rachel
Nolan, Trevor M.
Benfey, Philip N.
Ohler, Uwe
Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
title Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
title_full Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
title_fullStr Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
title_full_unstemmed Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
title_short Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
title_sort protocol for fast scrna-seq raw data processing using sckb and non-arbitrary quality control with copilot
topic Protocol
url 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
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