# ITS2 primers trimming without the primers sequences

**URL:** https://forum.qiime2.org/t/its2-primers-trimming-without-the-primers-sequences/18141
**Category:** General Discussion
**Tags:** its, dada2
**Created:** [January 19, 2021, 12:06pm UTC](https://forum.qiime2.org/t/its2-primers-trimming-without-the-primers-sequences/18141 "2021-01-19T12:06:57Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![Lavendel](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/l/ecccb3/32.png) [@Lavendel](https://forum.qiime2.org/u/Lavendel)
#### Post date: [January 19, 2021, 12:06pm UTC](https://forum.qiime2.org/t/its2-primers-trimming-without-the-primers-sequences/18141/1 "2021-01-19T12:06:57Z")

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The sequencing facility told me that their ITS2 primers are proprietary, so they cannot provide the sequences, but only the length of the primers. But, the sequences of the primers are needed to trim out the read-through to the opposite primers according to the ITS workflow ([Fungal ITS analysis tutorial](https://forum.qiime2.org/t/fungal-its-analysis-tutorial/7351) and [DADA2 ITS Pipeline Workflow (1.8)](https://benjjneb.github.io/dada2/ITS_workflow.html))

Is there any possibility to check if there are read-throughs and trim them out with only the length of the primers?

Thank you 😓

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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [January 19, 2021, 12:13pm UTC](https://forum.qiime2.org/t/its2-primers-trimming-without-the-primers-sequences/18141/2 "2021-01-19T12:13:11Z")

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Hi @Lavendel,  
See also the q2-itsxpress tutorial, this plugin can also handle readthrough and trimming to the ITS region, without knowing the actual primers:

> [@Q2-ITSxpress: A tutorial on a QIIME 2 plugin to trim ITS sequences](https://forum.qiime2.org/t/q2-itsxpress-a-tutorial-on-a-qiime-2-plugin-to-trim-its-sequences/5780):
>
> ITSxpress: a QIIME 2 plugin to trim ITS sequences Adam R. Rivers - USDA Agricultural Research Service Sveinn V. Einarsson - Dep. Microbiology and Cell Science, U. Florida & USDA Agricultural Research Service Background The internally transcribed spacer (ITS) region a widely used phylogenetic marker for fungi and other taxa. Previous work by [Nilsson et al. (2009)](https://doi.org/10.1111/j.1574-6968.2009.01618.x) showed that removing the conserved regions around the ITS results in more accurate taxonomic classification. An existing program, [ITS…](https://doi.org/10.1111/2041-210X.12073)

> [@Lavendel](#):
>
> The sequencing facility told me that their ITS2 primers are proprietary

That is very unfortunate. That is the antithesis of science, which should be reportable and reproducible by others. And causes so many problems like the one you are experiencing now! Fortunately, I think q2-itsxpress will save the day.

Let us know!

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### Author: ![Lavendel](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/l/ecccb3/32.png) [@Lavendel](https://forum.qiime2.org/u/Lavendel)
#### Post date: [January 19, 2021, 1:19pm UTC](https://forum.qiime2.org/t/its2-primers-trimming-without-the-primers-sequences/18141/3 "2021-01-19T13:19:28Z")

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Thank you very much! 😁

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### Author: ![Adam\_Rivers](https://forum.qiime2.org/user_avatar/forum.qiime2.org/adam_rivers/32/10143_2.png) [@Adam\_Rivers](https://forum.qiime2.org/u/Adam_Rivers)
#### Post date: [January 19, 2021, 7:41pm UTC](https://forum.qiime2.org/t/its2-primers-trimming-without-the-primers-sequences/18141/4 "2021-01-19T19:41:43Z")

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Yes, ITSxpress uses the edges of the ITS region (ITS1 or ITS2) so it does not need the primers.

If you need the primer sequences ( at least in the hybridizing regions) you can extract them using BBtools-BBmerge:

[https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmerge-guide/](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmerge-guide/)

```
bbmerge.sh in=reads.fq out=merged.fq adapters=adapters.fa

```