<p>Try this one</p>

<pre><code>for file in /dir/*
do
  cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG "$file" &gt;&gt; results.out
done
</code></pre>

<p>Also you have omitted <code>--discard-untrimmed</code> from the original command. If you want that as well along with everything to run in parallel:</p>

<pre><code>for file in /dir/*
do
  cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG --discard-untrimmed "<span class="math-container">$file" -o "`basename -s .fastq $</span>file`_out.fastq" &amp;
done
</code></pre>

CC BY-SA 4.0
2020-03-10T21:33:46.890Z
2020-03-12T14:20:38.600Z
2020-03-12T14:20:38.600Z
prab4th
<p>I have DNA sample from 5 pools, having 25 fastq files each. I am running cutadapt to remove the primers using this command 
<code>cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG A7_S7_R1_001.fastq -o sb_A7_S7_R1_001.fastq --discard-untrimmed</code>
However, this is too time consuming.  I tried my hand at writing shell script</p>

<pre><code>for file in /dir/*
do
  cmd cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG "$file" &gt;&gt; results.out
done
</code></pre>

<p>But it is not running . 
Can someone help.
Thanks</p>

CC BY-SA 4.0
2020-03-08T14:18:55.890Z
I assume you don't really have `cmd` in there. Put and `ls` in just to see which files are seen.
Devon Ryan
<fastq><shell><cutadapt>
processing multiple fastq files with cutadapt
# processing multiple fastq files with cutadapt

(Asked by: username_0 on 2020-03-08)

I have DNA sample from 5 pools, having 25 fastq files each. I am running cutadapt to remove the primers using this command 
cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG A7_S7_R1_001.fastq -o sb_A7_S7_R1_001.fastq --discard-untrimmed
However, this is too time consuming.  I tried my hand at writing shell script
for file in /dir/*
do
  cmd cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG "$file" >> results.out
done

But it is not running . 
Can someone help.
Thanks

**Tags:** fastq, shell, cutadapt
> **Comments:**
> **username_1**: I assume you don't really have `cmd` in there. Put and `ls` in just to see which files are seen.  

---

## 1 answers

### Answer by username_2 on 2020-03-10. Score: 2

Try this one
for file in /dir/*
do
  cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG "$file" >> results.out
done

Also you have omitted --discard-untrimmed from the original command. If you want that as well along with everything to run in parallel:
for file in /dir/*
do
  cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG --discard-untrimmed "$file" -o "`basename -s .fastq $file`_out.fastq" &
done


---

