Partek Flow Documentation

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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


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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