Question: Seurat scRNAseq analysis: what is the mito gene list
1
gravatar for wenbinm
22 months ago by
wenbinm20
USA
wenbinm20 wrote:

Hi there, I am trying to analyze 10X genomics output with Seurat. After reading in data using "Read10X" function and create an Seurat object, I am stuck at this step:

> mito.genes <- grep(pattern = "^MT-", x = rownames(x = my_data@data), value = TRUE)

For the data I have, row names of the expression matrix are gene names ("Sox17" "Mrpl15" "Lypla1" "Tcea1" "Rgs20" etc) or ensembl ID, where no genes begin with "MT-".

Does anyone know the mitochondria gene list Seurat uses for quality control? Or I should generate a mitochondria gene list on my own? I am working on mouse samples.

Many thanks for your help!

scrnaseq rna-seq • 3.5k views
ADD COMMENTlink modified 21 months ago by rogangrant10 • written 22 months ago by wenbinm20
1

Mouse mt gene ids will start with "mt-"

ADD REPLYlink written 17 months ago by Arup Ghosh2.7k
2
gravatar for igor
22 months ago by
igor11k
United States
igor11k wrote:

Looks like you have a mouse genome. Instead of ^MT-, you can look for ^Mt- or just add ignore.case = TRUE to the grep.

ADD COMMENTlink written 22 months ago by igor11k

It works. Thank you! It seems that Seurat is always using these 13 genes: 'Nd1','Nd2','Co1','Co2','Atp8','Atp6','Co3','Nd3','Nd4l','Nd4','Nd5','Nd6','Cytb'

ADD REPLYlink written 22 months ago by wenbinm20
1
gravatar for rogangrant
21 months ago by
rogangrant10
rogangrant10 wrote:

At least in my case, mouse mitochondrial genes are flagged with ^mt-, rather than ^Mt-. But either will still work if you set ignore.case = TRUE as per igor's suggestion.

ADD COMMENTlink modified 21 months ago • written 21 months ago by rogangrant10
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