Importing Feature Barcoding Data

• Create a new Project

• Import data

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

Figure 1. Create a new project and give it a meaningful name (e.g. CITE-Seq tutorial)

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

Figure 2. Import options for CITE-Seq tutorial data

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

Figure 3. Import options for CITE-Seq tutorial data

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)

Figure 4. File format options for MALT data set

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.

Additional Assistance

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