DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data.

ABSTRACT:

Background

Advances in droplet-based single-cell RNA-sequencing (scRNA-seq) have dramatically increased throughput, allowing tens of thousands of cells to be routinely sequenced in a single experiment. In addition to cells, droplets capture cell-free "ambient" RNA predominantly caused by lysis of cells during sample preparation. Samples with high ambient RNA concentration can create challenges in accurately distinguishing cell-containing droplets and droplets containing ambient RNA. Current methods to separate these groups often retain a significant number of droplets that do not contain cells or empty droplets. Additionally, there are currently no methods available to detect droplets containing damaged cells, which comprise partially lysed cells, the original source of the ambient

SUBMITTER: Muskovic W 

PROVIDER: S-EPMC8641258 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature