使用 scKB 和 COPILOT 进行快速单细胞 RNA-seq 原始数据处理的方案。

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.

机构信息

Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany.

Department of Biology, Duke University, Durham, NC 27708, USA.

出版信息

STAR Protoc. 2022 Dec 16;3(4):101729. doi: 10.1016/j.xpro.2022.101729. Epub 2022 Sep 30.

DOI:10.1016/j.xpro.2022.101729

PMID:36181683

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9530667/

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).

摘要

我们描述了一个使用 scKB 和 COPILOT 对单细胞 RNA 测序 (scRNA-seq) 原始数据进行快速和非任意质量控制的方案。scKB 是 kallisto 和 bustools 的包装脚本，用于加速对齐和转录物计数矩阵的生成，其运行速度明显快于流行的 Cell Ranger 工具。COPILOT 然后通过比较低质量和高质量细胞的分布来提供非任意的背景噪声去除。总的来说，该方案简化了处理工作流程，为新的 scRNA-seq 用户提供了一个简单的入口。有关使用和执行此方案的完整详细信息，请参阅 Shahan 等人。(2022)。