low ribosomal protein in scrnaseq data
Hi,
10X genomics has provided some info about expected ribosomal proteins based on the cell type in single cell data this link. I wanted to ask if removal of cells with very low ribosomal proteins (eg less than 5 percent) is required during pre-processing? I am dealing with samples from benign colon tumors in mice and in majority of the cells (nearly half of the cells) the ribosomal protein percent is less than 5 percent.
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10X gives a little insight into this: https://kb.10xgenomics.com/hc/en-us/articles/218169723-What-fraction-of-reads-map-to-ribosomal-proteins
Just scan through the PCs and see if there is one that contains mainly Ribosomal proteins
Well, I asked for clarifications when the percent of ribosomal proteins are low and also provided the 10X link in my question.