Importing Feature Barcoding 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

Under the Data tab, click Import data
Click Import single cell data
Choose the filtered HDF5 file for the MALT sample produced by Cell Ranger

If you have already moved the .h5 file to where Partek Flow is installed, choose the Partek Flow Server radio button and browse to its location. If you have downloaded the .h5 file to your local machine, choose the My computer radio button and upload the file through your web browser. 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

Figure 2. 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 94). If Ensembl 94 is not available from the drop-down list, choose Add annotation and download it.
Uncheck Report features without counts
Click Finish (Figure 3)

Figure 3. 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

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

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Import data

Additional Assistance