Hi, I would greatly appreciate your help with the following question.

I am running R to analyze CITE-seq data which includes both protein and RNA expression profiles. I use Seurat Multimodal vignette to run the analysis. For total cells, this vignette works great. I am able to look at both protein and gene expression from clusters. When I try to make subsets, I found that expression level of certain gene is really low, which makes it very difficult to make such subset based on gene expression. So, I am thinking to gate on protein (for example, CD8+granzymeB+(positive) or vs CD8+granzymenB-(negative) cells), make subset and look for the gene expression profile of this subset. Could you please help with this using Seurat-compatible vignette. Thanks so much for the help.