Obtain and add files to the project

The sample used for this tutorial can be found in the 10x Genomics Datasets. We will use the Control, replicate 1 mouse brain sample. 

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The fastq files will be imported into the project as a unaligned reads node. 

Pre-processing the unaligned fastq files

The unaligned reads must be preprocessed before proceeding with the analysis steps covered here: Spatial data analysis. 

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For more information about Space Ranger click here.

Annotate Visium image

To run Annotate cells:

• Click a Single cell counts data node
• Click the Pre-analysis tools section in the toolbox
• Click Annotate Visium image

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