# Reads processing with different primers

**URL:** https://forum.qiime2.org/t/reads-processing-with-different-primers/2777
**Category:** User Support
**Tags:** taxonomy, feature-classifier, dada2, taxa, trim, primers, deblur
**Created:** [January 29, 2018, 9:39pm UTC](https://forum.qiime2.org/t/reads-processing-with-different-primers/2777 "2018-01-29T21:39:56Z")
**Posts on this page:** 1
**Showing post:** 7

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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 31, 2018, 3:05pm UTC](https://forum.qiime2.org/t/reads-processing-with-different-primers/2777/7 "2018-01-31T15:05:30Z")

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@Lu_Yang,

> [@Lu\_Yang](#):
>
> About the trimming the longer reads to the overlapped region, such as 515f-806r. May I know are there any code or protocol can be used in QIIME2 or others? Thanks.

Yes, you can use q2-cutadapt to trim your demultiplexed reads prior to denoising. See [this tutorial](https://forum.qiime2.org/t/demultiplexing-and-trimming-adapters-from-reads-with-q2-cutadapt/2313)

> [@Lu\_Yang](#):
>
> (3)I use the following command to merge the table, “qiime taxa collapse --i-table table.qza --i-taxonomy taxonomy.qza --p-level 7 --o-collapsed-table table-I7.qza”. I have tried, and indeed this will give the result table only at the species level, NOT at OTU level. And I think I will not continue try this procedure. BUT very informative for me. Thanks.

Yes that is the point — to collapse at species level (since OTUs from different primer regions will be unique even if they overlap). But I think we can all agree this is not the best solution for your case.

Regarding your questions about q2-fragment-insertion, you can check out [this post](https://forum.qiime2.org/t/q2-fragment-insertion-community-plugin/1967) about this community plugin, or perhaps @Stefan can answer your questions.

I hope that helps!

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