Fig. 1

The scATAC-pro workflow. The workbench consists of two units, data processing unit and downstream analysis unit. Modules of the data processing unit include demultiplexing and adaptor trimming of the raw reads, followed by mapping of reads to the reference genome and filtering of low-quality reads. Aggregated reads are used for generating genome browser tracks, peak calling, and cell calling. Quality check (QC) reports are generated based on both aggregated data and single-cell data. Modules of the downstream analysis unit consists of dimension reduction, clustering, differential accessibility between different cell populations, genome browser track generation per cell subpopulation, TF motif enrichment analysis, footprinting analysis, and prediction of chromatin interactions. Most modules provide more than one analysis methods