Fig. 1

Overview of AMULET. a Tn5 transposase cleaves accessible DNA at maternal and paternal chromosomes in each nucleus. Number of ATAC-seq read counts per genomic region per nucleus are expected to be 0, 1, or 2. b Instances where >2 overlapping reads are observed for any genomic region in a cell are identified using an efficient algorithm for counting the number of overlapping reads. c Poisson cumulative distribution function is used to detect multiplets based on deviations from expected number of genomic regions with >2 overlapping reads. d Overview of downstream analyses: (1) quantification of multiplet detection performances using artificial multiplets, (2) comparison of AMULET to alternative method ArchR, and (3) annotating cellular origins of multiplets using a clustering-based method