Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
STAR Protocols, ISSN: 2666-1667, Vol: 3, Issue: 4, Page: 101729
2022
- 5Citations
- 17Captures
- 1Mentions
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- Citations5
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- Captures17
- Readers17
- 17
- Mentions1
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COPILOT – fast scRNA-seq raw data processing using scKB and non-arbitrary quality control
Researchers from Humboldt Universität zu Berlin 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-
Article 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).
Bibliographic Details
http://www.sciencedirect.com/science/article/pii/S2666166722006098; http://dx.doi.org/10.1016/j.xpro.2022.101729; http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=85138996293&origin=inward; http://www.ncbi.nlm.nih.gov/pubmed/36181683; https://linkinghub.elsevier.com/retrieve/pii/S2666166722006098; https://dx.doi.org/10.1016/j.xpro.2022.101729
Elsevier BV
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