Estimating and correcting index hopping misassignments in single-cell RNA-seq data.

ABSTRACT: Index hopping causes read assignment errors in data from multiplexed sequencing libraries. This issue has become more prevalent with the widespread use of high-capacity sequencers and highly multiplexed single-cell RNA sequencing (scRNA-seq) libraries. We conducted deep, plate-based scRNA-seq on a mixed population of mouse skin cells. Analysis of transcriptomes from 1152 cells identified four distinct cell types. To estimate the error rate in sample assignment due to index hopping, we employed differential expression analysis to identify signature genes that were highly and specifically expressed in each cell type. We quantified the proportion of misassigned reads by examining the detection rates of signature genes in other cell types. Remarkably, regardless of gene expression levels, we e

SUBMITTER: Miao L 

PROVIDER: S-EPMC11527012 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature