High number of detected genes per cell after doublet removal - scRNAseq data
Hi,
I have used doubletFinder to remove doublets from scRNAseq data but still a considerable proportion of cells have high nFeature_RNA (> 6000) while based on the quality control violin plots the median nFeature_RNA is between 2000 to 3000. Should I still remove the skewed cells in terms of number of detected genes after using doubletFinder?
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sarahmanderni
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Please show plots, or anything. Also, what is the experimental design? Are there many celltypes expected with very different numbers of expressed genes?
Here are the violin plots after removal of doublets. These are four samples from mouse lung tumor.
Also, could you please make an example about when there could be many cell types with very different number of expressed genes? do you mean differentiated and non-differentiated cell types?