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Old 08-23-2017, 11:57 AM   #10
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Originally Posted by pmiguel View Post
If you are running these on a non-patterned-flowcell Illumina sequencer, ignore the primer peaks. If you are running them on a patterned-flowcell Illumina sequencer (HiSeq 3000/4000/X and NovaSeq) then do an extra ampure (or whatever small fragment clean-up you have available to you.)

Hello Phillip,
Can you explain your reasoning behind the difference between patterned and non-patterned flowcells?

I can see how primers that contain an index sequence might lead to more index hopping on patterned flowcells, but what would be the issue with these primers that donít contain an index sequence?
I have noticed these primer peaks with Kapa kits before since they use a high concentration of PCR primers to prevent exhaustion, but I have never sequenced the libraries on a patterned flowcell. Now Iím curious to see if this is going to be an issue on the NovaSeq.

Thank You
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