Import Peak Count Matrix

Several formats can be imported into a Peak Count Matrix (Image peak_count_matrix_16_n_p) using the following importers:

The importers can be found here:

        Import (Image Next_Folder_16_n_p) | Single Cell Data (Image single_cell_importers_16_n_p) | Import Peak Count Matrix (Image import_cell_clonotypes_16_n_p)

The importers can be used in workflows. See On-the-fly import in workflows for details.

General options

Image atac_import_general_options
Figure 4.9: The Cell Ranger Peak Count importer. The General options are common to all the peak matrix importers.

The following options are common to all peak matrix importers (figures 4.9 and 4.10):

The data to be imported may either consist of peak data only or it may be a mixture of peaks and gene expressions, as is the case for 10x Multiome files. In the latter case, the gene expressions must be imported into a separate Expression Matrix (see Import Expression Matrix).

HDF5 importer

The Cell Ranger HDF5 importer requires one file to be supplied:

MEX importer

The MEX importer requires three files to be supplied:

See https://math.nist.gov/MatrixMarket/formats.html for details of the Matrix Market Exchange Coordinate Format.