Pros/cons of cell hashing

Question

[bleven]

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!

Answer 1

[igor]

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.