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Note: when using the Space Ranger task in Partek Flow, there are more restrictions on the sampe sample name-- sample name can only contain letters, digits, underscores and dashes. Please Edit the sample names on Data tab in Partek Flow to remove any other characters, e.g. space etc.

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If this is the first time you are using Space Ranger or Cell Ranger, you will need to create a Cell Ranger reference (Figure 2).

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The result of Space Ranger task is the Single cell counts data node, which contains the gene expression data. Double click the Single cell counts node to invoke the report the task report (Figure 6) which is the same as the ‘Summary HTML’ from the original 10x Genomic pipelines. Task report is sample based. You can use the dropdown list in top left to switch samples (not shown in Figure 6).  Each report consists of two pages: Summary and Analysis. For details, please visit 10x Genomics web page.

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You can find the location of the <project-name>_spatial.zip file using the following sepssteps. Selcte Select the Space Ranger task node (i.e. the rectangle) and then click on the Task Details (toolbox). Click on the Output files link to open the page with the list of files created by the Space Ranger task. Mouse over any of the files to see the directory in which the file is located. Figure 9 shows the path to the .zip file which is required for Annotate Visium image.

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