cell_ranger_arc

• count

  Aligns and quantifies FastQ files from a 10X snRNA+ATAC-seq experiment against a reference genome. Output matrices are provided in triplet and h5 formats.
• make_libraries_csv

  Creates a sample sheet for a whole project, listing the sample names, assay types and paths to FastQ files. It can be subset to produce a sample sheet for a sample.
• mkref

  Creates an index for use with Cell Ranger ARC. It can produce custom genomes if provided with the relevant (and correctly formatted) FastA and GTF files.