An important challenge in pre-processing data from the 10x Genomics Chromium platform 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 the power to identify real cells and rare subpopulations, we introduce CB2, a cluster-based approach for distinguishing real cells from background barcodes.

CB2 distinguishes cells from background barcodes in 10x Genomics data