# Import multiplexed R1.fastq and R2.fastq with mixed forward and reverse reads + truncate reverse primer

**URL:** https://forum.qiime2.org/t/import-multiplexed-r1-fastq-and-r2-fastq-with-mixed-forward-and-reverse-reads-truncate-reverse-primer/2052
**Category:** User Support
**Tags:** pending-development, import, primers, cutadapt
**Created:** [December 1, 2017, 8:09pm UTC](https://forum.qiime2.org/t/import-multiplexed-r1-fastq-and-r2-fastq-with-mixed-forward-and-reverse-reads-truncate-reverse-primer/2052 "2017-12-01T20:09:20Z")
**Posts on this page:** 1
**Showing post:** 9

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### Author: ![Martin](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/m/73ab20/32.png) [@Martin](https://forum.qiime2.org/u/Martin)
#### Post date: [December 27, 2017, 3:19pm UTC](https://forum.qiime2.org/t/import-multiplexed-r1-fastq-and-r2-fastq-with-mixed-forward-and-reverse-reads-truncate-reverse-primer/2052/9 "2017-12-27T15:19:14Z")

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Hi there,

I am very excited to see that qiime2 2017/12 includes a new feature to trim forward and reverse primers. Apparently, you were quite busy during Christmas.

I was testing the preliminary [q2-cutadapt tutorial](https://forum.qiime2.org/t/demultiplexing-and-trimming-adapters-from-reads-with-q2-cutadapt/2313), which works fine 👍

Now I wanted to trim the forward primer from my demultiplexed sequences using "qiime cutadapt trim-single", however, this did not worked so far. I used to following command:

qiime cutadapt trim-single   
--i-demultiplexed-sequences DemuxSeq.qza   
--p-cores 4   
--p-front CCTACGGGNGGCWGCAG   
--p-match-read-wildcards   
--p-match-adapter-wildcards   
--p-error-rate 0   
--o-trimmed-sequences trimmed-seqs.qza   
--verbose \

The command does not return any error, it is simply running forever. However, the CPU is idle and no memory is used. I stopped it after a while with ctrl + c.

In the following you see a screenshot, showing the first bases of my sequences (including forward primer: CCTACGGGNGGCWGCAG) in fastq format.

 ![Screenshot from 2017-12-26 13-22-09](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/1X/938e47097403fa032de92affabaa21b4ca22150d.png)

Well... its open for discussion and suggestions 🙂

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_[View the full topic](https://forum.qiime2.org/t/import-multiplexed-r1-fastq-and-r2-fastq-with-mixed-forward-and-reverse-reads-truncate-reverse-primer/2052)._