I know I am not the brightest in this topic, but I believe this question should not be that stupid.
Is there (generally speaking) a qualitative way to compare 2 workflows of scRNA seq, which only differ in their mitochondrial cutoffs?
I followed the workflow from the seurat vignettes "Guided tutorial" , "SCTransform" and "Integrate Data" and when it came to this code:
pbmc <- subset(pbmc, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5)
I entered one time 30% for the mitochondrial cutoff and another time 20%.
I did this analysis in two distinct projects, but every other step is identical.
If it's possible, are there some criterias to qualitative compare the results (UMAPs, found marker genes) or does this need additional analysis steps?