I am completing a meta-analysis on data that has different hypervariable regions. I understand that guidelines require that closed reference OTU picking be performed, because one can not compare different hypervariable regions to each other.
However, I am curious as to why researchers cannot run de novo OTU picking on a single study, assign taxa to the OTU (using QIIME or other means), then combine the results after assigning taxa. To me, this would result in a reduced loss of data compared to closed reference OTU picking, but I don’t know what other implications might occur. Is there some sort of bias that occurs because of this? Or other problems that I don’t see?
Also, I had not seen how to merge results after FeatureTable[Frequency (table.qza.) and FeatureData[Sequence] (rep-seqs.qza), at least in QIIME 2. If anyone knows how to merge taxa tables, I would like to try both ways mentioned above to see what results are produced.
I hope my explanation made sense. If required, I can provide a list of commands that I would use to perform the two separate analyses above to better explain what I am trying to say.
Thank you for your help. I look forward to your response.