# Cutadapt doesn't recognize all adapter sequences

**URL:** https://forum.qiime2.org/t/cutadapt-doesnt-recognize-all-adapter-sequences/17609
**Category:** Technical Support
**Tags:** cutadapt
**Created:** [November 26, 2020, 5:59pm UTC](https://forum.qiime2.org/t/cutadapt-doesnt-recognize-all-adapter-sequences/17609 "2020-11-26T17:59:11Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![llenzi](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/l/9fc29f/32.png) [@llenzi](https://forum.qiime2.org/u/llenzi)
#### Post date: [December 2, 2020, 12:10pm UTC](https://forum.qiime2.org/t/cutadapt-doesnt-recognize-all-adapter-sequences/17609/2 "2020-12-02T12:10:57Z")

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Hi @elephas,

Welcome on the forum!  
If you have not fixed the issue yet, I would suggest you to trim the PCR primers instead of the sequencing adapters, which should  
be following the adapter sequences in your reads (although it may depend on the library prep used).

Also, I suggest you to look at the following thread:

> [@Remove Primer in paired-end demultiplexed file](https://forum.qiime2.org/t/remove-primer-in-paired-end-demultiplexed-file/17376/12):
>
> Hi @mohsen_ej, Thank you for attaching the QZVs. You'll want to add the following flags, which were also mentioned in the posts I linked above: --p-match-adapter-wildcards --p-match-read-wildcards --p-discard-untrimmed You'll likely not need --p-match-read-wildcards, but it does not hurt to throw it in. baseball This will allow cutadapt to match the IUPAC codes in your primers (i.e. W, V N,...) with the reads, and discard any sequences in which it could not find both primers. The latter en…

and add '--p-match-adapter-wildcads' and '--p-discard-untrimmed' as options!

Hope it helps

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