Differences in the percent clusters passing filter on patterned and non patterned flow cells
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Instruments that use patterned flow cells have artificially lower percent clusters passing filter (%PF) metrics compared to non-patterned flow cells.
With patterned flow cells, there is no template generation or preliminary filtration step during image analysis, which results in lower %PF values.
Because template generation and the associated preliminary filtration steps are not applied, all nanowells, including empty wells or clusters that may be dim, low quality, or polyclonal are included in the raw cluster count, which leads to lower %PF values.
The uniform feature sizes and optimal spacing in the patterned flow cell enable significantly increased cluster density for patterned flow cells, ultimately resulting in a greater yield capacity.
Although the percent passing filter metric is generally lower with patterned flow cells, it does not negatively impact performance or data quality.
Consult the specifications for the instrument and sequencing configuration to evaluate run performance, quality, and data output.
For further information, see the technical note Calculating Percent Passing Filter for Patterned and Nonpatterned Flow Cells.
For any feedback or questions regarding this article (Illumina Knowledge Article #7457), contact Illumina Technical Support .