You can try to set the –p-trim-length -1 (no trim) to have a see. The bigger number you set, the fewer reads you will have.
In Deblur your joined reads should be trimmed based on the quality scores, check out the tutorial Alternative methods of read-joining in QIIME 2 — QIIME 2 2018.2.0 documentation, also the post [Deblur vs DADA2 Questions] @antgonza referred to.
Now, IMOO it’s really hard to make direct comparisons between the 2 methods, mainly because of the error models
I am not sure about that, but the huge drop in total frequencies made me little wary of the Deblur method.
is that demux.qzv doesn’t have the same initial input as the other 2. Is this expected? Perhaps you can try using the same inputs.
I had to re-import my fastq files after removing "underscores" from filenames in order to use Deblur which seemed to be sensitive to "_" . This is why the inputs may looked a bit different, but overall they are pretty much comparable.
Also, out of curiosity, what’s the results if you use --p-trim-length 240 in deblur?
Using a trim-length 240 we see an increase in total frequency from ~14,000 up to ~55,000 but that still too far from ~234,000 total frequency in DADA2. deblur-stats-240.qzv (192.2 KB)
Thanks for your comments!