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!