CB2 – a cluster-based approach for distinguishing real cells from background barcodes in droplet-based scRNA-seq experiments

An important challenge in pre-processing data from droplet-based single-cell RNA sequencing protocols is distinguishing barcodes associated with real cells from those binding background reads. Existing methods test barcodes individually and consequently do not leverage the strong cell-to-cell correlation present in most datasets.

To improve cell detection, researchers at the University of Wisconsin-Madison have developed CB2, a cluster-based approach for distinguishing real cells from background barcodes. As demonstrated in simulated and case study datasets, CB2 has increased power for identifying real cells which allows for the identification of novel subpopulations and improves the precision of downstream analyses.

Overview of CB2


a Projection of a hypothetical cell population containing three subpopulations (red, green, and blue where intensity corresponds to read depth). CB2 takes as input a gene by barcode matrix of UMI counts and returns a gene by cell matrix. b High-count barcodes with counts above a pre-specified upper threshold are considered real cells; barcodes with counts below a lower threshold are used to estimate a background distribution. The remaining barcodes are clustered, and tight clusters are tested as a group against the estimated background distribution; barcodes not in tight clusters are tested individually (not shown). High-count barcodes and those identified by CB2 are retained for downstream analysis

Ni Z, Chen S, Brown J. (202) CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data. Genome Biol 21, 137. [article]

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