Hi
I need help with dada2 parameters. I’m not sure if I am choosing the best trim&trunc for the data.
I used 16s V3-V4 and the amplicon size expected is ~460bp.
these are the primers:
16S Amplicon PCR Forward Primer = 5’
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG
16S Amplicon PCR Reverse Primer = 5’
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC
I used cutadapt plugin to remove the primers and adapters and asked you about them in another topic Remove Primer
what’s your mind about identifying dada2 parameters for this file
Thank you very much in advance
Please see my response to your question in Remove Primer in paired-end demultiplexed file. It looks like you didn’t actually remove the primers, so I’m not so sure it would make sense to run dada2 on data that still contain non-biological sequences.
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