Dear Qiime2 community,
I have a question about a data analyses procedure.
I have a set of 500 samples from whom ITS1 and ITS2 have been amplified.
I've analyzed them without merging these two dataset because I read that in this case, it could give false positive or create chimeric sequences.
I performed taxonomic classification on both ITS1 and ITS2 dataset with the Qiime release of UNITE database version 9 (2023-07-18) containing all Eukaryotic sequences.
After this step, I compared the ITS1 and ITS2 classification by looking at how many UNITE IDs were shared between the two dataset and I found that 350 ASVs have been classified as the same.
My question is: can I merge ITS1 and ITS2 if I remove these shared ASVs from one of the dataset?
I was thinking that maybe I will not be able to use those matrices that take phylogeny into account, but perhaps Jaccard or Bray-Curtis are still applicable.
Also, if this is a correct procedure, do you think that it mght be worthed useing just this database for the data analyses?
Thank you so much for your help and opinions!!