Overall success rate: after filtering by FinalmCReads, mCCCFrac, R1MappingRate, we usually got ~80% wells (or cells) remaining. The success rate between MiSeq and NovaSeq should be very close. If the MiSeq success rate is below 65% (< 2000 success in a total of 3072), I do not recommend proceeding to NovaSeq. There must be some quality issues either during FACS or due to the library preparation.