Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.
Journal Article (Journal Article)
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).
- Hsu, C-W; Shahan, R; Nolan, TM; Benfey, PN; Ohler, U
- December 2022
Volume / Issue
- 3 / 4
Start / End Page
- 101729 -
Pubmed Central ID
Electronic International Standard Serial Number (EISSN)
International Standard Serial Number (ISSN)
Digital Object Identifier (DOI)