filtering gene sets when performing scRNAseq data analysis
I am trying to analyze scRNAseq data and perform marker detection and DGE analysis comparing different conditions. to do so I filtered out some sets of genes including sex chromosome related ones and mitochondrial ones. do I need filter out Ribosomal protein genes (starting with "RP")? what else should be filtered out?
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Why do you think that anything should be filtered by category? High expression of these genes might indicate ongoing processes that define a cell. You should remove genes with very low counts or those only expressed in few cells.