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I am running Seurat on publicly available dataset of ~400k cells. More than 80% of the cells are returned as NA when I use percentageFeatureSet(object, pattern = "^MT-"). How should I interpret these result? Does this mean the 80% of cells are of poor quality or have no mitochondrial content?
Any help would be greatly appreciated. Zahra
I do have MT genes.
Update: The data was not downloaded intact. Thank you for your help!