Hi, I have a question about how to output a .qzv file after denoise. Because I want to generate plots for quality scores after denoise and comparing to the original quality score.
The denoise command lines I use is:
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux-paired-end_demodata.qza
–p-trim-left-f 25
–p-trim-left-r 7
–p-trunc-len-f 220
–p-trunc-len-r 200
–o-representative-sequences rep-seqs-dada2.qza
–o-table table-dada2.qza
–o-denoising-stats satats-dada2.qza
–p-n-threads 24
Is it right if I want to generate a quality score after this procedure by using:
qiime demux summarize
–i-data rep-seqs-dada2.qza
–o-visualization rep-seqs-dada2.qzv
Disclaimer: I’m not part of the official QIIME 2 team, so please take my answer with a huge grain of salt.
If I understand your question correctly, you are wondering whether it’s possible to create a plot that shows read quality score – like this one from the Moving Pictures tutorial – after denoising with DADA 2. If so, that’s an interesting question!
However, I don’t think that’s possible (or useful) because the output of DADA 2 is an amplicon sequence variant (ASV) table and by definition, ASVs are sequences that already take account noises from the sequencing machine by learning the error rate with quality score. Since the quality score is used to make ASVs, I don’t think ASVs themselves would have per-base quality score as the input sequence reads would do (and therefore not comparable).
That being said, I suppose you could compare read quality score between your original sequence reads vs. filtered sequence reads that will be ultimately used by DADA 2 to inform ASVs. This is because DADA 2 performs read filtering/trimming before building the error model (see the Filter and trim section in this tutorial from DADA 2).
Again, I think above is different from what you originally had in your mind since here, sequence reads have not been “denoised” yet; they are just filtered and trimmed. Also, I’m not sure whether you can access those filtered/trimmed sequence reads winin the QIIME 2 platform (i.e. you may have to run the DADA 2 program outside of QIIME 2).
Hope this helps. I’m sure the official QIIME 2 team will give you better guidance. I just thought your question was interesting
