I am performing differential gene expression analysis of single-nuclei RNA-seq data with DESeq2 and pseudobulk counts per cell type. 3 groups, 4 samples per group.
The nuclei vary to some extent concerning their mitochondrial RNA counts. So, DESeq2 naturally produces the most significant genes to be mitochondrial.
Is there a way to include this as a covariate in the design formula or somewhere else and provide an additional column "percent.mitochondrial.RNA" in the colData?
Thank you, best, Chris