Merging ITS1 & ITS2 primers: a question about methods

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!!

1 Like

Yes, but there's going to be big trade-offs involved in working with different regions.

Justing made a table about working with multiple regions and what to expect:

This sounds like the column 'Genus-level taxa' from Justine's table.


Dear @colinbrislawn,
Thank you for your prompt response. I found Justine's table to be very informative and useful!