Calculating percentage of ribosomal genes in single cell data

Question

[kenneditodd]

I have seen Rps and Rpl genes, ribosomal proteins, used to calculate the proportion of ribosomal reads in QC for scRNAseq. Should mitochondrial ribosomal proteins, Mrps and Mrpl genes, be included? What about ribosomal RNA genes?

Answer 1

[rpolicastro]

For mitochondrial percentage people usually use the genes on the mitochondrial chromosome. In most genomes this chromosome will be chrMT or MT. This is roughly a measure of cell health because apoptotic or lysed cells will tend to have a higher percentage of reads derived from the mitochondrial genome.

For ribosomal percentage it's usually the genes distinguished by the gene_biotype designation of rRNA in most references, which is separate from the mitochondrial rRNA which is denoted by Mt_rRNA.

I haven't seen many people use ribosome proteins specifically for scRNA-seq QC because they are transcribed by Pol II and thus expected to be captured by poly-dT priming. People are generally more interested in rRNA because it makes up ~95% of total rRNA, and should be selected against by poly-dT priming and template switching. A high percentage of rRNA could indicate some problem with library prep of that cell or some cell quality issue.