# RE: raw paired sequences were mixed

**URL:** https://forum.qiime2.org/t/re-raw-paired-sequences-were-mixed/17886
**Category:** General Discussion
**Created:** [December 28, 2020, 8:32am UTC](https://forum.qiime2.org/t/re-raw-paired-sequences-were-mixed/17886 "2020-12-28T08:32:59Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![yhuizhen](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/y/46a35a/32.png) [@yhuizhen](https://forum.qiime2.org/u/yhuizhen)
#### Post date: [December 28, 2020, 8:32am UTC](https://forum.qiime2.org/t/re-raw-paired-sequences-were-mixed/17886/1 "2020-12-28T08:32:59Z")

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> [@raw paired sequences were mixed](https://forum.qiime2.org/t/raw-paired-sequences-were-mixed/17865/2):
>
> Hello @yhuizhen, Yes, lots of other people have also had this problem, but the good news is that [the cutadapt plugin now supports mixed orientation reads](https://docs.qiime2.org/2020.11/plugins/available/cutadapt/demux-paired/)! Adding --p-mixed-orientation to your qiime cutadapt demux-paired command should allow you to import these reads as shown in the [cutadapt tutorial](https://forum.qiime2.org/t/demultiplexing-and-trimming-adapters-from-reads-with-q2-cutadapt/2313). Let us know if you have any questions! Colin

hi,Colin, I don't find the correct way to identify the mixed sequences using cutadapt in qiime2. Could you show me one example??  
In my raw r1.fq, there are 515F primer from the far left, and 806R primer from the seventh base. The first 6 bases may be the adapter.  
515F (5′-GTGCCAGCMGCCGCGGTAA-3′)  
806R (5′-GGACTACHVGGGTWTCTAAT-3′)  
attached one snapshot below:

 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/8/8a11155f8890d5ef46287d08d4cd4cd579ee3a92.png)

Kayla

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### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 28, 2020, 8:17pm UTC](https://forum.qiime2.org/t/re-raw-paired-sequences-were-mixed/17886/2 "2020-12-28T20:17:30Z")

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### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 28, 2020, 8:17pm UTC](https://forum.qiime2.org/t/re-raw-paired-sequences-were-mixed/17886/3 "2020-12-28T20:17:53Z")

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A post was merged into an existing topic: [raw paired sequences were mixed](https://forum.qiime2.org/t/raw-paired-sequences-were-mixed/17865)

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### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 28, 2020, 8:23pm UTC](https://forum.qiime2.org/t/re-raw-paired-sequences-were-mixed/17886/4 "2020-12-28T20:23:35Z")

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