Sequencing using P7 adaptor

[abbecker]

Illumina (MiSeq):

Let' say I have multiple amplicon samples, generated by PCR, that look like:

P7Adapt - pad - Index - pad - GenSpecificPrimerF - ...... - GenSpecificPrimerR - pad - Index2 - pad - P5Adapt

Could I sequence them using the P7Adapt+pad sequence? Instead of having to run mutiple runs and sequence with pad+GenSpecificPrimer each time?

[jwfoley]

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.