I need you to help me with a a few general questions. Thanks in advance!
In general, once I have a qza file, what commands can be used to convert it to qzv file that can be visualized in qiime2 view? After recalling what I have done so far with qiime2, it looks like both the “qiime feature-table summarize” and “qiime demux summarize” can do the job. But what is the difference? I should have some misunderstanding of qiime2 basic concepts.
I have some 16s data to analyze, and I understand there might not be a standard operating procedure for qiime2 analysis. Please correct me if there is. I thought it all depends on what analysis you are going to do and how you do it. But this makes me a bit less confident of what I have done. Did I do it right? Here is my workflow and I would greatly appreciate if anyone could correct me if I miss anything or did not do it in the right order:
–Trimming adapter and primer sequence
–dada2 denoising (will produce rep seqs)
–filtering samples and features
–generating taxonomy.qza file (using rep seqs file)
–alpha/beta diversity analysis
–generating taxa bar plot
After filtering samples and features, should I redo dada2? because filtering will remove some OTU and some samples, so representative sequences generated from the dada2 step will not be representative anymore, right?
Thank you very much.