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

• Cell Hashing features must have a different data type than your gene expression or protein expression data
• Cell Hashing data should be normalized with CLRData node contains number of features less than number of observations
• Data node must be output from normalization task (recommended normalization method for hashtag is CLR)

If you are processing your FASTQ files in Partek Flow, be sure to specify a different Data type for your Cell Hashing FASTQ files on import than the FASTQ files for your gene expression and any other antibody data. 

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If you want to specify sample IDs instead of using hashtag feature IDs as the sample IDs, you will need to prepare a tab-delimited text file (.txt) with hashtag feature IDs in the first column (Hashtag) and the corresponding sample IDs in the second column (Sample) (Figure 1). A header row is required. 

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