Ahh was looking at the wrong table ... - wow - using cutadapt to trim everything to the same size per primer sites really slaughters my resulting sequences after clean up!
allprimers-cutadaptTrim-table.qzv (667.1 KB)
My entire Pro dataset is essentially gone...guess it makes sense I essentially cut off 174 bps off the front of the Pro sequences to make them match up with the primer start sites of Arc and V4 and in looking at the demux - the 'before' trim looks great...
Pro-pe-demux.qzv (287.4 KB)
The after trim...took a dive off a quality cliff in what's left and I assume dada2 just axed most of it...
Pro-pe-demux-primerTrim.qzv (292.6 KB)
Good to know. q2-insertion (rather than cutadapt to primer sites) is the way to go (at least with these datasets) when analyzing fragments of different lengths. Knew that going in but now I can show the PI and it adds to the discussion from these forum topics: