Partek Flow supports the import of filtered gene-barcode matrices generated by 10x Genomics' Cell Ranger pipeline. The following document will illustrate how to perform this import.
Below is a video summarizing the import of these files:
To import the matrices into Partek Flow, create a new project and click Import > Import scRNA count feature-barcode-mtx.
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Samples can be added using the Add sample button. Each sample should be given a name and three files should be uploaded per sample using the Browse button.
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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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There are folders nested within the matrix folder, typically representing the reference genome it was aligned to. Navigate to the lowest subfolder, this should contain three files:
Select all 3 files for importing into Partek Flow
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Specify the annotation file used when running the pipeline.
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Click Finish when you have completed configuration. This will queue the import task.
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 and select multiple matrices to import in batch. To import an h5 matrix, select the 
Import scRNA full count matrix or h5 option. Browse for the files and modify any configuration options.
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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 the folder and select all the matrices you would like to import.
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Configure all the relevant sample metadata, including sample name and the annotation that was used to generate the matrices, and 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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