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Create a new Project

Let's start by creating a new project.

On the Home page, click New project (Figure 1)
Give the project a name
Click Create project

Flow Documentation > Importing Feature Barcoding Data > Screenshot 2023-09-07 at 14.28.39.png

Import data

In the Analyses tab, click Add data
Click 10x Genomics Cell Ranger counts h5 (Figure 2)
Choose the filtered HDF5 file for the MALT sample produced by Cell Ranger

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Move the .h5 file to where Partek Flow is installed using , then browse to its location.

Flow Documentation > Importing Feature Barcoding Data > Screenshot 2023-09-07 at 14.34.20.png

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 109). If Ensembl 109 is not available from the drop-down list, choose Add annotation and download it.
Check Features with non-zero values across all samples in the Report section
Click Finish (Figure 3)

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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.