qiime2 version: 2020.6
Data: 16S rRNA metagenome 2x250 sequences from Illumina MiSeq. 12 Samples from various sites of the human body(skin, oral, some negative controls, etc.).
Problem: Low read count after merging and denoising paired end reads with dada2.
Trimming is performed with the qiime2 cutadapt implementation, trimming both forwards and reverse V3-V4 primers and also the reverse version of them from the opposite directions.
As it can be seen, the sequence quality is not good, and not much of an improvement is achieved after trimming (demux summary before trimming not shown).
I have done a little bit of research and from what i found, usually it is suggested to use only the forward reads, when low read count is achieved after denoising/merging, but in this case, as it can be seen from the demux summary, the forward reads look even worse than reverse reads.
Trying different --p-trunc-len-f/r parameters made little to no changes.
Question: Is the quality of the reads in this case the most likely reason for low count after denoising/merging?
Should i only use reverse or forward reads or what other options do i have?
Any help would be greatly appreciated.