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?
What I'd recommend doing is running demux summarize to get the interactive sample detail for your first run. You can examine this plot and see where the quality score drops below 20 and use that bp position for your other runs.
Thank you for your reply! Yes, looking at the plots was what I did. I just thought there was some handy way to get dada2 to tell me where it decided to cut.
Not in QIIME 2 directly - if you wanted to automate that process you'd need to create some sort of external Python script that would pull out that information (most likely from the demux summary table) in a systematic way.
