I have single cell RNA-seq from PBMCs. Cellranger gives a mean reads per cell by dividing the total number of reads by the estimated number of cells. After loading into Seurat I can get the true mean reads per cell by taking the mean of nCount_RNA.
For the 5 samples I have, the mean reads from Cellranger are between 30k and 98k. The mean nCount_RNA is between 4100-4800.
Is this normal? Where are most of the sequencing reads going, is this from sequencing RNA from burst cells?