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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. and Shahan, R. and Nolan, T.M. and 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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