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Import data

• Under the Data tabIn the Analyses tab, click Import Add data
• Click Import single cell data 10x Genomics Cell Ranger counts h5 (Figure 2)
• Choose the filtered HDF5 file for the MALT sample produced by Cell Ranger

Move the .h5 file to where Partek Flow is installed using , then choose the Partek Flow Server radio button and browse to its location. Otherwise, select the URL radio button and paste in the following link (Figure 2):http://cf.10xgenomics.com/samples/cell-exp/3.0.0/malt_10k_protein_v3/malt_10k_protein_v3_filtered_feature_bc_matrix.h5

Note that Partek Flow also supports the feature-barcode matrix output (barcodes.tsv, features.tsv, matrix.mtx) from Cell Ranger. The import steps for a feature-barcode matrix are identical to this tutorial. 

• Click Next
• Name the sample MALT (the default is the file name)
• Specify the annotation used for the gene expression data (here, we choose Homo sapiens (human) - hg38 and Ensembl Transcripts release 94109). If Ensembl 94 109 is not available from the drop-down list, choose Add annotation and download it.
• Uncheck Report features without countsCheck Features with non-zero values across all samples in the Report section
• Click Finish (Figure 3)

A Single cell counts data node will be created under the Analyses tab after the file has been imported. We can move on to processing the data.

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