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Multimodal reference mapping on subsets #4465

Answered by rsatija
erosix asked this question in Q&A
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Just to add a bit more context - Azimuth does support the mapping of single cell types (or subsets of cells) to a complex reference. We have successfully tested taking isolated populations of T cells and mapping them to the reference, and we only map to T cells.

If you are getting a result where most cells map to T cells but some others do map to other cell types, we would suggest isolating cells that map - for example - to monocytes, and asking what genes are differentially expressed in these cells. If there are any monocyte or non-T markers, that would be evidence of contamination.

It is quite common to see contaminating cells, either due to FACS contamination, or alternately, doublet c…

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