Fig. 1

Evaluating the performance of CellRanger-arc (cR). A Histogram of the fraction of reads in peaks (FRiP) of all droplets for sample A. Nuclei containing droplets are located within the bell curve and in the right tail of the distribution. The CellRanger-arc threshold (vertical red line) rejects more than half of the nuclei within the bell curve. B CellRanger-arc count threshold. A scatter plot shows the number of log(ATAC) reads (x-axis) versus the unique log(RNA) reads (y-axis) for each droplet, and we observe a continuum in the distribution of counts. Nuclei that pass CellRanger-arc’s count threshold are plotted in blue, and those that fail this threshold are plotted in pink. C Histogram of a linear combination of logarithmic counts that is constant along the k-means line. We see a continuum at the location of the threshold (vertical red line)