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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 (Figure 1) for each sample. 

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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. 

Choose to import 10x Genomics Visium Space Ranger output for your project (Figure 2).

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• Click Transfer files on the homepage, under settings, or during import (Figure 3). import 

Proceed to transfer files as shown below using the 10x Genomics Visium Space Ranger outputs importer (Figure 3).

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• Navigate to the appropriate files for each sample (Figure 4). Please note that the 10x Genomics Space Ranger output can be count matrix data as 1 filtered .h5 file per sample or sparse matrix files for each sample as 3 files (two .csv with one .mtx or two .tsv with one .mtx for each sample). The spatial output files should be in compressed format (.zip). The high resolution image can be uploaded and is optional. 

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Count matrix files and spatial outputs should be included for each sample (Figure 4). Once added, the Cells and Features values will update. 

Once the download completes, the sample table will appear in the Metadata tab, with one row per sample (Figure 5).

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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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