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To run Hashtag demultiplexing, your data must meet the following criteria:1)

• Cell Hashing features must have a different data type than your gene expression or protein expression data

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• Cell Hashing data should be normalized with CLR

If you are processing your data using Cell Ranger, be sure to specify a different feature_type for your Cell Hashing antibodies than any other antibodies in the Feature Reference CSV File. 

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Running Hashtag demultiplexing

• Click the Normalized counts data node for your cell hashing data
• Click Hashtag demultiplexing in the Pre-analysis tools section of the toolbox
• Click Browse to select your Sample ID file (Optional)
• Click Finish to run

The output is a Dumultiplexed counts data node. Two cell-level attribute, Cells in droplet and Sample of origin, are added by this task and are available for use in downstream tasks. You can download the attribute values for each cell by clicking the Demultiplexed counts data node, clicking Download, and choosing to download Attributes only. 

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