# dada2 merging and comparing different data sets

**URL:** https://forum.qiime2.org/t/dada2-merging-and-comparing-different-data-sets/18326
**Category:** General Discussion
**Tags:** dada2, merge
**Created:** [February 1, 2021, 5:38pm UTC](https://forum.qiime2.org/t/dada2-merging-and-comparing-different-data-sets/18326 "2021-02-01T17:38:03Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [March 7, 2021, 8:39pm UTC](https://forum.qiime2.org/t/dada2-merging-and-comparing-different-data-sets/18326/2 "2021-03-07T20:39:20Z")

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Hello Alya,

Welcome to the forums! 👋 Sorry to keep you waiting on an answer. It's been quite the February!

> [@Alya\_Heirali](#):
>
> Is it appropriate to compare the two data sets given these differences?

Yes! See this great [discussion on GitHub](https://github.com/benjjneb/dada2/issues/716) about processing data from multiple runs.

> [@Alya\_Heirali](#):
>
> I tried cutting the ROMA2 reads to 142,140 to make them more comparable but had difficulties merging my forward and reverse reads.

As long as the region sequenced is the same _after_ merging, you can pick the `truncLen` settings that work best for your data! See this comment from the dev:

> It's fine to use different `truncLen` parameters as long as the read pairs still overlap and are mergable at the end. The `truncLen` setting doesn't affect the merged amplicon region, it just affects the amount of overlap between the two reads.

I think the method you describe here should work great! 👍

* * *

> [@Alya\_Heirali](#):
>
> Is it appropriate to merge ASVs belonging to the same species?

That's a good question. I think the consensus on the Qiime 2 forums is to keep your ASVs separate for most downstream analysis so that you can make use of their subspecies resolution. However, it could be convenient to talk about 'species' instead of 'ASVs of the species' in the discussion section, and I like to merge features by taxonomy when I make stacked bar plots. 📊 🤷‍♂️ Your call!

Let us know if you have any other questions!  
Colin

P.S.

> [@Alya\_Heirali](#):
>
> Any thoughts/tips would be much appreciated.

👉 [Microbiome Datasets Are Compositional: And This Is Not Optional](https://www.frontiersin.org/articles/10.3389/fmicb.2017.02224/full)

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