Overlapping cluster/annotation · Biostar

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Overlapping cluster/annotation

Dear Senior Fellows,

I used Seurat to cluster my single cells and use singleR for annotation, but there seems to be an overlapping cluster / annotation. Are they doublets? or just error with annotation (circle in red). if they are doublets, is there any standard workflow in seurat I could remove them from seurat object! thank you before hand.

Kind Regards,
Synat,

enter image description here

single-cell

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updated 2.9 years ago by LChart

• written 2.9 years ago by synat.keam •

1 answer

I don't see any colored points corresponding to those labels (no yellow dots under "Chondrocytes", nothing looking green near "HSC_-G-CSV". What are the proportion/counts of these cell types in the overall dataset? If they're <1% of the total; I'd consider removing or reannotationg potentially. Or is this a subset of a much larger pool of cells (i.e., one donor from an experiment with dozens?)

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written 2.9 years ago by LChart

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