SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

• Published in: Gigascience Vol. 9; no. 12
• Main Authors: Young, Matthew D, Behjati, Sam
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 26.12.2020
• Subjects: Base Sequence; Biological effects; Contamination; Data acquisition; Data analysis; Datasets; Droplets; Gene expression; Gene Expression Profiling; Gene sequencing; Nucleotide sequence; Quality control; Ribonucleic acid; RNA; RNA - genetics; Sequence Analysis, RNA; Single-Cell Analysis; Technical Note; Transcriptome; Transcriptomics; pre-processing; scRNA-seq; decontamination

Abstract Background Droplet-based single-cell RNA sequence analyses assume that all acquired RNAs are endogenous to cells. However, any cell-free RNAs contained within the input solution are also captured by these assays. This sequencing of cell-free RNA constitutes a background contamination that c...