What causes a low % of mapped reads to cells?

  • Updated

Typical percentages are 40 % or more.

A number of reasons may be the cause of a low % of mapped reads to cells:

Reason Suggested Resolution
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.
Share this article:

Was this article helpful?

0 out of 0 found this helpful

Have more questions? Submit a request