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Navigate to the folder containing your filtered matrices. By default, the Cell Ranger pipeline output will have a folder called filtered_gene_bc_matrices.

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Select all 3 files for importing into Partek Flow and click Next

Specify the annotation file used when running the pipeline. If desired, the sample name can also be modified. 

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The Cell Ranger pipeline can also generate the same filtered gene barcode matrix in h5 format. This gives you the ability to select just one file per matrix. To import an h5 matrix, simple select the h5 file when selecting a file for import and click Next. This will take you to the same configuration page listed above.

This feature is also useful for importing multiple samples in batch. Simply put all h5 files from your experiment on a single folder, navigate to that and select all the matrices you would like to import.

Configure all the relevant sample metadata, including sample name and the annotation that was used to generate the matrices, click Finish when completed. Note that all matrices must have been generated using the same reference genome and annotation to be imported into the same project.

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