ScCensus: Off-target scRNA-seq reads reveal meaningful biology.

ABSTRACT: Single-cell RNA-sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity. Although scRNA-seq reads from most prevalent and popular tagged-end protocols are expected to arise from the 3^' end of polyadenylated RNAs, recent studies have shown that "off-target" reads can constitute a substantial portion of the read population. In this work, we introduced scCensus, a comprehensive analysis workflow for systematically evaluating and categorizing off-target reads in scRNA-seq. We applied scCensus to seven scRNA-seq datasets. Our analysis of intergenic reads shows that these off-target reads contain information about chromatin structure and can be used to identify similar cells across modalities. Our analysis of antisense reads suggests that these reads can be

SUBMITTER: He D 

PROVIDER: S-EPMC10862729 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature