Hello,
I have 16s V3-V4 data (skin microbiome). Unfortunately, the reverse reads are of poor quality so I decided to use dada2 Denoise-single.
My 80 samples are split across 5 different sequencing runs (unfortunately). Since dada2 should be trimmed at equal length across all samples and sequencing runs, I plan to do the following:
1.) Unfortunately the first run is the poorest in quality but - if I'm not mistaken - the "worst" run sets the cutting point for all the other one.
So I decided to use the --p-trunc-q 20 function of the dada2 denoise single, which works fine.
My question: Where can I find the exact position where dada2-p-trunc decided to cut so I can manually copy paste this position for the other four runs?
Thanks in advance!