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Old 01-29-2018, 02:34 PM   #2
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Location: Stanford

Join Date: Jun 2009
Posts: 181

If I understand your diagram correctly, and I'm not sure I do, the default read 1 (no custom primers) will be from the third pad leftward, into GenSpecificPrimerR and beyond, and then the default read 2 will be from the second pad rightward, into GenSpecificPrimerF and beyond. So if you don't mind sequencing your primers (and there's enough base diversity in them to avoid screwing up the cluster detection), paired-end reads should already be getting you what you want.
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