# ITS data analysis : How to determine which dada2 analysis is the best

**URL:** https://forum.qiime2.org/t/its-data-analysis-how-to-determine-which-dada2-analysis-is-the-best/18149
**Category:** User Support
**Tags:** dada2
**Created:** [January 20, 2021, 3:12am UTC](https://forum.qiime2.org/t/its-data-analysis-how-to-determine-which-dada2-analysis-is-the-best/18149 "2021-01-20T03:12:22Z")
**Posts on this page:** 1
**Showing post:** 6

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### Author: ![ChrisKeefe](https://forum.qiime2.org/user_avatar/forum.qiime2.org/chriskeefe/32/1907_2.png) [@ChrisKeefe](https://forum.qiime2.org/u/ChrisKeefe)
#### Post date: [January 22, 2021, 12:54am UTC](https://forum.qiime2.org/t/its-data-analysis-how-to-determine-which-dada2-analysis-is-the-best/18149/6 "2021-01-22T00:54:43Z")

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> [@YuZhang](#):
>
> The amplified fragments length of ITs varied greatly

This is an important consideration with ITS, and it's great that you're thinking about it. How much length variation is there in _your_ sequences?

The impact of these varying lengths is often significant in cases of readthrough (where you capture non-target nucleotides on "the outside" of the primer), and in cases where sequences are kept or dropped unfairly due to length.

Readthrough can be managed by trimming properly with cutadapt. This is discussed at some length [here](https://forum.qiime2.org/t/fungal-its-analysis-tutorial/7351). DADA2 could be involved in dropping sequences, but your DADA2 results show a high rate of sequence recovery, with no prominent bottlenecks where you're losing a lot of reads.

> [@YuZhang](#):
>
> I don’t think the difference between the three attempts was great.

I agree. You seem to be getting similar results from single-end and paired end runs, with slightly different parameters.

> [@ChrisKeefe](#):
>
> How well do you understand what DADA2 does, and how to use it?

You haven't answered my question above, and I'm not entirely clear on what your concern is with these results. Are you just uncertain about how to select DADA2 parameters? Do you think something problematic is happening in DADA2 specifically? Or just in general? If so, what do you think might be causing the unexpected results?

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