I want to know if is it possible to export the reads after processing them with dada2 (from the table.qza) and create something like fastaq files of each sample with the denoised reads?
You can then export any
qiime tools export.
As for specifically making fastq files after DADA2, once you have
FeatureData[Sequence] artifacts (often named
rep-seqs.qza), you have that information in a more compact representation which is generally more useful (also the quality scores are no longer needed).
So we don’t really have a way to turn that back into fastq files for each sample as it wastes a lot of space (it’s easier to keep track that you’ve seen a sequence 1000 times than it is to literally repeat that sequence 1000 times).
What is your overall goal? There may be another way to get you the data you’re looking for.
My goal is to classify my sequences using RDP (this is done on another program to test it and i want to use the same processed files used on QIIME2) to check if there´s a difference in the classifications of my sequences compared to the ones classified with silva128 on QIIME2 and create an interactive graphs using Krona per sample.
Perfect, then you don’t need a fastq file for each sample, rather the fasta file you get from
qiime tools export should be sufficient, since your interest is how taxonomy gets assigned to each sequence, the particulars of how many and which samples they belong to isn’t relevant.
This is the part we don’t have a great answer for, as you will need the feature-table and the taxonomy. There’s another thread exploring Krona, but I don’t think it made it to a final solution.
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