Cell Hashing enables sample multiplexing and super-loading in single cell RNA-Seq isolation by labeling each sample with a sample-specific oligo-tagged antibody against a ubiquitously expressed cell surface protein. 

The Hashtag demultiplexing task uses an algorithm developed by the Satija lab¹ to identify what sample each cell comes from and whether it is a multi-sample doublet.  

Prerequisites for running Hashtag demultiplexing

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

2) 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. 

If you are processing your data 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. 

Running Hashtag demultiplexing

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