from STARsolo to get the fraction of intronic UMI per cell (referred to as the nuclear fraction). We identified empty droplets with default DropletQC parameters (nf_rescue = 0.50, umi_rescue = 1000). We identified droplets with scds’s hybrid algorithm using the function cxds_bcds_hybrid to estimate doublet scores and called doublets on cells with scds.hybrid_score > 1.0. We identified damaged cells with high percentage of mitochondrial UMI counts using only miQC which uses a Bayesian EM algorithm to learn the relationship between mitochondrial UMI counts and number of captured genes. We used the posterior probability cutoff of 0.75 to call damaged cells by miQC.
