Dada2 trimming question

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If you compare the start of your sequences to the Illumina adapter/primer sequences, you will see they match in the second-half:

                                 CCTACGGG
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG

                                  NACTAC
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC

Those are the 341F and 805R primers, and they need to be removed. You can do so here with trim-left-f 17 and trim-left-r 21, which you can read off the above.

This amplicon is longer than the reads, so they won't read into the other primer, hence trunc-len is not needed for primer removal.

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