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Cell Ranger - ATAC task in Partek® Flow® includes two different wrappers. To deal with the single cell ATAC-Seq dataset, the 'cellranger-atac count' pipeline from Cell Ranger ATAC v2.0[2] has been wrapped in Flow®. It takes FASTQ files from 'cellranger-atac mkfastq' and performs ATAC analysis including reads filtering and alignment, barcode counting, identification of transposase cut sites, peak and cell calling, and count matrix generation. Its outputs then become the starting point for downstream analysis for scATAC-Seq data. To process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data,  ‘cellranger-arc count’ v2.0[3] has been wrapped to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage.

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