<p>After trying on my own this is the solution I came up with.
My solution was to use a pipe of the stderr into a new file.</p>
<pre><code>bowtie2 --local --threads 4 -x reference_genome.fa -f -U inputdata.fa -S OutputData.sam --no-hd --no-sq --no-unal -k 5 2&gt; 'bowtie2_summary/inputdata.txt'
</code></pre>

CC BY-SA 4.0
2021-07-02T22:53:26.967Z
2021-07-03T09:26:57.783Z
2021-07-03T09:26:57.783Z
Stephan
<p>BowTie2 puts out summary info to the terminal but doesn't allow me to save each to a separate file. How can I go about saving the output of BowTie2 so that MultiQC can read it and create a website from it?</p>

<bowtie2>
How to export summary data from Bowtie2 for MultiQC to read?
# How to export summary data from Bowtie2 for MultiQC to read?

(Asked by: username_0 on 2021-07-02)

BowTie2 puts out summary info to the terminal but doesn't allow me to save each to a separate file. How can I go about saving the output of BowTie2 so that MultiQC can read it and create a website from it?

**Tags:** bowtie2

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## 1 answers

### Answer by username_0 on 2021-07-02. Score: 2

After trying on my own this is the solution I came up with.
My solution was to use a pipe of the stderr into a new file.
bowtie2 --local --threads 4 -x reference_genome.fa -f -U inputdata.fa -S OutputData.sam --no-hd --no-sq --no-unal -k 5 2> 'bowtie2_summary/inputdata.txt'


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