ATAC Pipeline

The DRAGEN Single-Cell ATAC (scATAC) Pipeline can process single-cell ATAC-seq data sets from reads to a cell-by-peak read count matrix. The pipeline includes the following functions:

ATAC-seq alignment
Cell-barcode error correction for the barcode read
Chromatin accessibility peak calling
Fragment counting per cell and peak to measure chromatin accessibility
Sparse matrix output and QC metrics

The functionality and options related to alignment and gene annotation are identical to DNA pipelines. For information, see DRAGEN DNA Pipeline.