NA values for mitochondrial gene percentage
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@65e4eddd
Last seen 2.9 years ago
United States

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

Seurat scRNAseq • 1.8k views
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swbarnes2 ★ 1.4k
@swbarnes2-14086
Last seen 7 hours ago
San Diego

It means that none of the gene names begin with "MT-".

Can you confirm that the mitochondrial genes for your species do indeed begin with "MT-"?

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I do have MT genes.

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Update: The data was not downloaded intact. Thank you for your help!

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