Why are some cells of Cell type A located in Cell type B in scRNA-seq clustering?
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16 months ago

Hi all,

I have a question about the scRNA-seq clustering. In my data or some paper, although Cell type A and B are different cell types and are located far away in UMAP, some cells of Cell type A located in Cell type B. Take my UMAP as an example, Astro4 (green) clusterd well with other Astrocyte cluster, but some cells of Astro4 located in Microglia clusters (topright).

enter image description here

I think this is caused by a doublet issue or low capture efficiency or something...but I'm not sure...

How best to explain this phenomenon?

Thank you,

Joonhong

Clustering scRNA-seq snRNA-seq UMAP • 616 views
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Clustering is commonly done on the principal components while UMAP is a different algorithm, so some discrepancy is not unexpected. It would also depend on what the colors are based on, is this clusters as in the graph-based clustering, or something else? HArd to comment without details.

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I performed the analysis by following the seurat integration tutorial. This method is graph-based clustering.

That figure show only astrocyte clusters among all brain cells using subset function.

https://satijalab.org/seurat/articles/integration_introduction.html

Thank you.

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