Hello. Long time unregistered reader, first time poster.
I hope i chose the most appropriate category. Also, i`m only asking these questions because if failed to find the answers elsewhere online.
Can the ‘qiime cutadapt trim-paired’ plugin handle degenerate primer bases. For example: can i provide the whole 341F primer (CCTACGGGNGGCWGCAG) for the ‘–p-adapter-f’ parameter or should i only provide the part with no degenerate bases (CCTACGGG)?
Kind of a similar question the the first one. Can the ‘qiime feature-classifier extract-reads’ plugin handle primers with degenerate bases in them or should i provide only the part of the primer with no degenerate bases? Extracting from ‘SILVA 132’ database.
Should one cluster the feature table to ‘–p-perc-identity 97/99’ using ‘qiime vsearch cluster-features-de-novo’ before using the ‘qiime feature-classifier classify-sklearn’ plugin? What could be the advantages/disadvanges of doing so? Feature table prepared with ‘DADA2’.