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Pros/cons of cell hashing

Hello, I am running cells stimulated by two different proteins on 10x. I am trying to figure out If I should do hashtagging or not? Can someone outline the pros/cons? What they usually do/prefer? Thanks!

rna-seq 10x hashtagging

1 answer

It really depends on your experiment. Most people prefer the cost advantage, since you can run multiple samples in a single library. The benefits are described in the cell hashing paper:

Cell hashtags allow for robust sample multiplexing, confident multiplet identification, and discrimination of low-quality cells from ambient RNA.

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