Extended Data Fig. 7: Comparison of scifi-RNA-seq, droplet-based scRNA-seq and multi-round combinatorial indexing in terms of cell doublet rates. | Nature Methods

Extended Data Fig. 7: Comparison of scifi-RNA-seq, droplet-based scRNA-seq and multi-round combinatorial indexing in terms of cell doublet rates.

From: Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

Extended Data Fig. 7

a, Alignments to the mouse genome versus alignments to the human genome for each species mixing experiment, assessing the frequency of cell doublets for the different methods. Data are shown on a linear scale, normalized to UMIs per million to allow the use of common thresholds across experiments. Cells were classified as doublets if (i) there was less than twice as many UMIs aligning to one species’ genome than to the other species’ genome, or (ii) more than 75 UMIs per million were detected in both species. Doublet cells are highlighted in red. The grey line indicates x=y after accounting for species bias. The green lines indicate the threshold value of 75 UMIs per million. b, Same visualization as in panel a, but plotted on a logarithmic scale. c, Percentage of cell doublets for each method, corresponding to the red cells in panels a and b. d, Single-cell purity plotted for doublet cells only. Purity was calculated as the cell’s number of UMIs for the dominant species divided by its total number of UMIs.

Back to article page