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)

General options

Image atac_import_general_options
Figure 4.6: 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 4.6 and 4.7):

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).

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.

MEX archive importer

The MEX archive importer is provided for convenience. It accepts a .zip, .tar or .tar.gz archive file containing the files required by the MEX importer. In order to uniquely identify each file, these must have a specific name:

Image atac_import_mex_archive_peak_options
Figure 4.8: Options for nearby genes and transcription factors for the MEX archive importer

The nearby genes and/or transcription factors can be passed in as separate files as is common to all the importers.

Alternatively, they can be included in the archive file. Then that should be indicated with checkbox "Archive has peak annotations" respectively "Archive has peak-motif associations". The file names must match a specific pattern:

This can be relevant for importing an archive produced by the peak matrix exporter using compression (see Export Peak Count Matrix). It may also be necessary when passing multiple files to a batching or iterating workflow (see Chromatin Accessibility and Expression Analysis from Matrix).