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Old 04-23-2020, 04:53 AM   #6
ATϟGC
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Location: Canada

Join Date: Jun 2013
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If these are amplicon libraries and you want to minimize the amount of PhiX you can add "stagger" or "offset" nucleotides between the illumina sequencing primer region (like the nextera or truseq tail) and your locus-specific primer in order to create diversity of bases. These stagger nucleotides can also be added to restriction-digests adapters to increase base diversity.

I always add staggers to my amplicon primers and sequence multiple amplicons per run to increase diversity but I still always add 5-12% Phix just to be sure.
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