When ecvi = 1, we assume that Pr(bcvi|g, ecvi) follows Supplementary Table 4. ecvi is assumed to follow Bernoulli (10−qcvi10) where qcvi is a phred-scale quality score of the observed base call. We use the standard 10X pipeline to process the raw reads which estimates the phred-scale quality score based on the alignment of each read to the reference human transcriptome using the STAR aligner49.
