# How to remove primers and contaminants when using two pairs in multiplex?

**URL:** https://forum.qiime2.org/t/how-to-remove-primers-and-contaminants-when-using-two-pairs-in-multiplex/19846
**Category:** User Support
**Tags:** dada2
**Created:** [June 9, 2021, 10:58am UTC](https://forum.qiime2.org/t/how-to-remove-primers-and-contaminants-when-using-two-pairs-in-multiplex/19846 "2021-06-09T10:58:33Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [June 9, 2021, 3:14pm UTC](https://forum.qiime2.org/t/how-to-remove-primers-and-contaminants-when-using-two-pairs-in-multiplex/19846/2 "2021-06-09T15:14:56Z")

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Hi @vln21, welcome to :qiime2:!

You can simply enter multiple primers as summarized here:

> [@q2-cutadapt output](https://forum.qiime2.org/t/q2-cutadapt-output/17031/24):
>
> Good news @jessica.song! I think I solved this. fireworks First, thank you for sending me the PDF describing the protocol. I noticed a key statement: pairs of primers (Fw-Rev or Rev-Fw) had to be present in the sequence fragments That is, this particular sequencing facility must expect mixed orientation reads. rotating_light Therefore you need to enter in both primers for each of the --p-front-\* commands (in 5' - 3' orientation). dna Like so: qiime cutadapt trim-paired \ --i-demu…

More specifically, you can try the following:

```auto
qiime cutadapt trim-paired \
  --i-demultiplexed-sequences paired-end-demux.qza \
  --p-cores 4 \
  --p-front-f GATCGAGAAGACCCTRTGGAGCT GACGAGAAGACCCTAWTGAGCT \
  --p-front-r AAATTACGCTGTTATCCCT GGATTGCGCTGTTATCCCT \
  --p-match-read-wildcards \
  --p-match-adapter-wildcards \
  --p-discard-untrimmed \
  --o-trimmed-sequences paired-end-demux-primer-trimmed.qza \
  --verbose > cutadapt-log-2.txt

```

Then you can denoise.

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