I am working with a non model organism which has an annotated reference genome and a seperate mitochondrial genome as both fasta and gtf files in ncbi. The mitochondrial genes are not of part of the reference genome and I was wondering how I can go about identifying the cells with high mitochondrial reads in seurat. I usually only align my reads (not using 10x genomics) to the reference genome and do the downstream analysis on seurat. Should I somehow combine the mt genes into the reference?
Would appreciate your help if anyone have suggestions.
Thank you
data.filt <- data.filt[!grepl("^MT-", rownames(data.filt)), ]