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Old 09-07-2017, 07:19 AM   #8
Genetic Librarian
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Location: Europe

Join Date: May 2017
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The reported cluster density is not always reliable.
If a run is massively overclustered, the MiSeq can not distinguish single clusters and logically can not count them reliably.
Another indicator is the PhiX Alignment. If you spiked in 1%, but your SAV only reports 0,2% aligned, you might have overloaded your library 5-fold.

https://support.illumina.com/content...0-2014-038.pdf
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