Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes.
Nat Methods
; 17(6): 615-620, 2020 06.
Article
in En
| MEDLINE
| ID: mdl-32366989
ABSTRACT
Methods to deconvolve single-cell RNA-sequencing (scRNA-seq) data are necessary for samples containing a mixture of genotypes, whether they are natural or experimentally combined. Multiplexing across donors is a popular experimental design that can avoid batch effects, reduce costs and improve doublet detection. By using variants detected in scRNA-seq reads, it is possible to assign cells to their donor of origin and identify cross-genotype doublets that may have highly similar transcriptional profiles, precluding detection by transcriptional profile. More subtle cross-genotype variant contamination can be used to estimate the amount of ambient RNA. Ambient RNA is caused by cell lysis before droplet partitioning and is an important confounder of scRNA-seq analysis. Here we develop souporcell, a method to cluster cells using the genetic variants detected within the scRNA-seq reads. We show that it achieves high accuracy on genotype clustering, doublet detection and ambient RNA estimation, as demonstrated across a range of challenging scenarios.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
RNA
/
Single-Cell Analysis
/
RNA-Seq
Type of study:
Diagnostic_studies
Limits:
Humans
Language:
En
Journal:
Nat Methods
Journal subject:
TECNICAS E PROCEDIMENTOS DE LABORATORIO
Year:
2020
Document type:
Article
Affiliation country:
United kingdom