Can you please help me in a technical issue? We sent some samples to single cell sequencing The company says
Many of the reads were not assigned to cell-associated barcodes. This could be caused by high levels of ambient RNA or by a significant population of cells with a low RNA content, which the algorithm did not call as cells. The latter case can be addressed by inspecting the data to determine the appropriate cell count and using --force-cells.
This would happen if the cells aren’t transcriptionally active – but as these are PBMCs this is unusual .
Have you ever heard about such a problem? Any solution in this case? sending more sample of each patient for sequencing or comparing single cell with matched bulk RNA-seq which one help?
10X say they would do deep sequencing (covering the cost) to get something for us but I don't know why my boss says we should compare single cell with matched bulk RNA-seq.