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Old 03-26-2020, 10:58 AM   #3
cmbetts
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Location: Bay Area

Join Date: Jun 2012
Posts: 113
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It depends on your amplicon length and what you're trying to learn about it.

If it's shorter than ~500bp, you can amplify it directly with PCR primers with flanking Illumina adapter sequences, but you'll need to use some of the trickery of 16S protocols to stagger the base composition so that base calling doesn't go to crap.
If your amplicon is >300bp and you don't care about assembling individual amplicons, it would be technically easier and possibly cheaper to just treat it like gDNA with either Nextera or a fragmentation/ligation TruSeq-esque protocol because you can ignore the base complexity issues.
For longer amplicons, your only option is the Nextera or TruSeq type approach described above because you can't get reads long enough to stitch across the full sequence.
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