Typical percentages are 40 % or more.
A number of reasons may be the cause of a low % of mapped reads to cells:
|More than a 25 % fraction of primer dimers
|Check the Bioanalyzer traces, and quantify that the fraction of the product is at around 200 bp.
|Low emulsion stability leading to bulk-amplification
|Check the emulsion quality after Barcoding, and
verify that the DNA yields after the 1st PCR are < 4 ng/µL.
|The Cell Finder algorithm failed to accurately define the cutoff
|Review the Cell Finder plots.
|Overloading of cells into the cartridge
|Verify that the input concentration of cells does not exceed 4,000 cells/µL.