# Merging ITS1 & ITS2 primers: a question about methods
**URL:** https://forum.qiime2.org/t/merging-its1-its2-primers-a-question-about-methods/29142
**Category:** General Discussion
**Tags:** taxonomy, its
**Created:** [February 3, 2024, 1:46am UTC](https://forum.qiime2.org/t/merging-its1-its2-primers-a-question-about-methods/29142 "2024-02-03T01:46:21Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@Antani](https://forum.qiime2.org/u/Antani)
#### Post date: [February 3, 2024, 1:46am UTC](https://forum.qiime2.org/t/merging-its1-its2-primers-a-question-about-methods/29142/1 "2024-02-03T01:46:21Z")
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!!
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [February 3, 2024, 5:36pm UTC](https://forum.qiime2.org/t/merging-its1-its2-primers-a-question-about-methods/29142/2 "2024-02-03T17:36:49Z")
> [@Antani](#):
>
> My question is: can I merge ITS1 and ITS2 if I remove these shared ASVs from one of the dataset?
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:
> [@Using multiple 16s variable regions for analysis](https://forum.qiime2.org/t/using-multiple-16s-variable-regions-for-analysis/28833/5):
>
> Thanks for the tag @lizgehret! Yeah, I've spent a lot of time thinking about this in the last year. Attempting to write a paper, TBH, but its slower going than I expected. So, @Rakaya, like Liz said, the issue in directly combining the two regions is that you're not going to have an ID overlap if you only use the ASVs. Remember from [ESVs should replace OTUs](https://www.nature.com/articles/ismej2017119) that the ASV ID is that single nucleotide sequence. ASVs that differ by a single nucleotide are going to be identified as different, and so…
> [@Antani](#):
>
> looking at how many UNITE IDs were shared between the two dataset and I found that 350 ASVs have been classified as the same.
This sounds like the column 'Genus-level taxa' from Justine's table.
---
### Author:  [@Antani](https://forum.qiime2.org/u/Antani)
#### Post date: [February 4, 2024, 12:02am UTC](https://forum.qiime2.org/t/merging-its1-its2-primers-a-question-about-methods/29142/3 "2024-02-04T00:02:50Z")
Dear @colinbrislawn,
Thank you for your prompt response. I found Justine's table to be very informative and useful!