scATAC-pro consists of two units, the data processing unit and the downstream analysis unit. The data processing unit takes raw fastq files as input and outputs peak-by-cell count matrix, QC report and genome track files. It consists of the following modules: demultiplexing, adaptor trimming, read mapping, peak calling, cell calling, genome track file generation and quality control assessment. The downstream analysis unit consists of the following modules: dimension reduction, cell clustering, differential accessibility analysis, gene ontology analysis, TF motif enrichment analysis, TF footprinting analysis, linking regulatory DNA sequences with gene promoters, and integration of multiple datasets. We provide flexible options for most of analysis modules.

This tutorial will focus on