Odd-looking cell cycle scores in scRNA-seq data
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5 weeks ago
Igor ▴ 40

I've performed the cell cycle scoring using the scanpy workflow. When I visualise the phase I get the following plot:

enter image description here

It seems that some cells have a vastly differing profile from the rest. Because of this, I can't really tell if the majority of the cells are separable by the first two PCs. I haven't seen that many cell cycle scores before, does it look atypical? How would you go about investigating this?

scanpy single-cell rna-seq • 187 views
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The phases doesn't look too unusual to me. Even the PCA might be ok. Look into tSNE or UMAP and colour points by other QC metrics like number of UMIs, number of features, percentage mitochondrial expression etc.

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