I am analyzing some ITS sequences using this tutorial and I have some questions regarding trimming. After creating the demux.qza file, I used the qiime cutadapt trim-paired command to cut the adapters and got the demux-trimmed.qza file.
*qiime cutadapt trim-paired *
Then I proceeded to dada2 step with both non-trimmed demux.qza and trimmed demux-trimmed.qza to compare the results. My results from qiime dada2 denoise-paired were far from ideal (a high percentage of sequences failed to merge) so I also ran qiime dada2 denoise-single using only the forward reads. These analyses gave me a total of 4 options:
Where table no.1 (non-trimmed-single-end) is the table with the "best-looking" data, meaning that I could save the highest number of samples and use them in downstream analyses. While if I use the table no.4, I can do almost nothing with the data I have due to low feature count, and loss of too many samples in downstream analyses.
So my question is, may I proceed using my top choice table, or it is using the only the forward reads with non-trimmed adapters generally not a good idea? Is trimming an essential step even if it results in great loss of data?
For reference, my sequences are ITS2 region with ITS3 and ITS4 primers. The quality of sequences is pretty good (no need to trim or trunc in dada2).