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Space Ranger output files are pre-processed 10x Genomics Visium data. The steps covered here will show you how to import and continue analyses with this pre-processed data from the Space Ranger pipeline. Partek Flow refers to this high cellular resolution data as Single cell counts; each point (spot) can be 1-10 cell resolution depending on the tissue type*. 

Add files to the project

The project includes Human Colon Cancer (Replicate 1) and Human Colon Cancer (Replicate 2) output files in one project. 

• Obtain the filtered Count matrix files (h5 or HDF5) files and Spatial outputs for each sample

The spatial imaging outputs should be in compressed format. 

• Navigate the options to select 10x Genomics Visium Space Ranger output as the file format for input

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The sample table is pre-populated with sample attributes, # Cells. Sample attributes can be added and edited manually by clicking Manage in the Sample attributes menu on the left. If a new attribute is added, click Assign values to assign samples to different groups. Alternatively, you can use the Assign values from a file option to assign sample attributes using a tab-delimited text file. For more information about sample attributes, see here.

For this tutorial, we do not need to edit or change any sample attributes.

Resources

*  More about 10x Genomics Visium Spatial Gene Expression 

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