I am doing QC on the single-cell RNAseq data. I have 3 samples: tumor, normal, adjacent. All data shows strong right skewed distribution of # genes and # of cells or most cells have fewer genes. So right now, I only filtered out cells > 10 % mitochondrial percent and cell < 200 genes. I wonder should I increase the lower cutoff to filter out more cells, or should we have a higher cutoff to remove any multiplets (I do not if I need to do since it has tumor cells). I am using the
I do not know how to post images here, but I really appreciate if you can provide me any suggestion or guidelines or any paper to refer.
Thank you in advance.