Hi, I am analyzing some 16S V4 rRNA amplicon data from low-diversity symbiont communities, planning on using DADA2 in QIIME2. The issue I am having is that the quality of the forward reads is very poor, while the quality of the reverse reads is also bad but more usable and typical for reverse reads I think. Example sequencing run:
demux-paired-end.qzv (311.6 KB)
(the primer set results in an amplicon of ~400 bp, and the sequencing chemistry was 2x250 bp, so I'd expect ~100 bp overlap)
I'm not sure that DADA2 will be able to merge these, although I will attempt to run it in paired end mode and play with the parameters. But I suspect the forward reads might be too low quality to use at all, and I might want to denoise only the reverse reads. Is this possible in DADA2? I know that you can use only forward reads in the single end mode, but haven't found any info about using only reverse reads. I would appreciate any insight, thank you!