NA values for mitochondrial gene percentage

Question

[zahra.mesri95]

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

[ATpoint]

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)) ?

[zahra.mesri95]

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"  

[Wayne]

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

[zahra.mesri95]

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

[rpolicastro]

What is your exact line of code?

[zahra.mesri95]

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