I have 25 single cell RNAseq 10X samples processed with CellRanger. Three of these samples appear to be contaminated with high levels of low gene cells which are probably "soup" or loose mRNA. I want to filter out these low quality cells, but I don't want to also remove low expressing cells that I am interested in by raising the nFeature threshold too high.
Another bioinformatician in my lab suggested that I use the CellRanger filtered_feature_bc_matrix for these contaminated samples, rather than the raw_feature_bc_matrix. Is it advisable to use filtered_feature_bc_matrix for some of the samples and raw_feature_bc_matrix for the rest? Or should I use entirely one or the other?