Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT
Che‐Wei Hsu, Rachel Shahan, Trevor M. Nolan, Philip N. Benfey, Uwe Ohler
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).
Topics & Concepts
Protocol (science)Computer scienceWorkflowQuality (philosophy)Streamlines, streaklines, and pathlinesControl (management)Real-time computingDatabaseArtificial intelligenceEngineeringEpistemologyPathologyAerospace engineeringAlternative medicineMedicinePhilosophySingle-cell and spatial transcriptomicsCancer Genomics and DiagnosticsCancer-related molecular mechanisms research