Fig. 3

Characterization of barcode swapping in droplet-based scRNA-seq experiments. a The expected number of cells with shared cell barcodes in 10x Genomics samples that have been multiplexed for sequencing, for different numbers of samples and different numbers of captured cells per sample. The cell exclusion approach for barcode swapping would remove these cells. b A schematic of our method to remove swapped reads from droplet data. Reads found in different samples with the same combination of UMI, cell barcode, and aligned gene were considered to have swapped. If most reads (≥80%) were present in one sample, we excluded the molecule from all other samples (i). If reads were more evenly spread across samples, we excluded the molecule from all samples (ii). Reads in one sample only were retained (iii). c t-SNE plot of the expression profiles of mouse epithelial cells¹⁷. Each point represents a cell that is coloured by sample. Letters correspond to different experimental conditions while numbers represent biological replicates. d The distribution of the library sizes for called cells in each sample. Cells were called using emptyDrops, with an FDR threshold of 1% and a minimum of 1000 UMIs. e The number of called cells for each sample, before and after application of our swapped read exclusion algorithm