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NA values for mitochondrial gene percentage

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

na-values scrna-seq seurat
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written by zahra.mesri95 • zahra.mesri95

Are you even sure the gene names are HGNC so that you can use that pattern? What is the output of:

grep("^MT-", rownames(your_seurat_object), value=TRUE)

and

head(rownames(your_seurat_object)) ?

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written by ATpoint ATpoint

Yes, I do have MT genes.

Here is what I get:

grep("^MT-", rownames(scRNA), value=TRUE)
 [1] "MT-ND1"  "MT-ND2"  "MT-CO1"  "MT-CO2"  "MT-ATP8" "MT-ATP6" "MT-CO3" 
 [8] "MT-ND3"  "MT-ND4L" "MT-ND4"  "MT-ND5"  "MT-ND6"  "MT-CYB" 
> head(rownames(scRNA))
[1] "AL627309.1" "AL669831.5" "FAM87B"     "LINC00115"  "NOC2L"      "KLHL17"
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updated by GenoMax GenoMax • written by zahra.mesri95 • zahra.mesri95

What about case? I note here, they tried lowercase as well.

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written by Wayne Wayne

I did try lower case and returned character(0).

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written by zahra.mesri95 • zahra.mesri95

What is your exact line of code?

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written by rpolicastro rpolicastro

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

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written by zahra.mesri95 • zahra.mesri95

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