CellPlex CMO highbackground

Question

[TheCatalyst]

Is it possible to salvage a Cellplex CMO labeling if the fraction reads in cell-associated barcodes is about 40%? What am I missing? Thanks.

[bk11]

I am guessing that you aligned the data using CellRanger. CellRanger demultiplexes the samples using barcode based method (CMO/LMO). Yes, you can still assign the CMOs to samples using SNP based methods (like freemuxlet, scSplit, Souporcell, Vireo etc.). The methods discussed in the following links will help you rescue the CMOs.

Bioinformatics tools for sample demultiplexing

Demuxafy