Odd-looking cell cycle scores in scRNA-seq data

Odd-looking cell cycle scores in scRNA-seq data

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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

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