# Qiime 2 for Ion Torrent PGM 16S rRNA

**URL:** <https://forum.qiime2.org/t/qiime-2-for-ion-torrent-pgm-16s-rrna/1524>\
**Category:** User Support\
**Tags:** ion-torrent\
**Created:** [October 17, 2017, 4:32pm UTC](https://forum.qiime2.org/t/qiime-2-for-ion-torrent-pgm-16s-rrna/1524 "2017-10-17T16:32:17Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![Harry](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/h/f6c823/32.png) [@Harry](https://forum.qiime2.org/u/Harry)\
**Post date:** [October 17, 2017, 4:32pm UTC](https://forum.qiime2.org/t/qiime-2-for-ion-torrent-pgm-16s-rrna/1524/1 "2017-10-17T16:32:17Z")

</div>

My data is 16S rRNA seq using Ion Torrent PGM.

The length of ideal seqs should be 300~400, I need to delete seqs that are shorter than 300. In mothur, it is very simple to use a command minlength=300, I am wondering the command for Qiime 2.

I did not find command on the official tutorials, The reason I am posting here is that Qiime 2 always gives me errors...

Thanks a lot

---

<div class="post-metadata">

**Author:** ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)\
**Post date:** [October 17, 2017, 7:25pm UTC](https://forum.qiime2.org/t/qiime-2-for-ion-torrent-pgm-16s-rrna/1524/3 "2017-10-17T19:25:25Z")

</div>

Hey @Harry!

> [@Harry](#):
>
> The length of ideal seqs should be 300~400, I need to delete seqs that are shorter than 300. In mothur, it is very simple to use a command minlength=300, I am wondering the command for Qiime 2.

If you were to use `dada2` for your processing, the equivalent parameter would be `trunc-len`.

Also based on [this note](https://github.com/benjjneb/dada2/issues/67#issuecomment-239340866) it looks like you should set `trim-left` to at least 15 for Ion Torrent data.

Let me know if you need more details!

P.S. Out of curiosity, what format is the output in from an Ion Torrent sequencer? Do our current import commands work, or is this a pain-point?

---

<div class="post-metadata">

**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\
**Post date:** [November 18, 2017, 1:25am UTC](https://forum.qiime2.org/t/qiime-2-for-ion-torrent-pgm-16s-rrna/1524/5 "2017-11-18T01:25:46Z")

</div>

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.