I am using Nanopore to sequence 16S/23S in a microbiome study. I am about to start looking at my sequencing data (removing adapters, trimming data) and found myself unsure whether both strands of the amplicons are fed into the nanopore (and therefore if I should search for both forward and reverse primer sequences in both directions). I can't find a clear answer to this.
If anyone could enlighten me, I would greatly appreciate it.
Best,
Sofie
What kit are you using? I wouldn't be surprised if your enrichment protocol had a nested design with both reverse and forward primers as is the tradition. This is the property of the enrichment kit, not to be confused with the ability of nanopores to be able to sequence both strands of the enriched amplicon akin to that of paired-end sequencing of Illumina.
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