Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-02T22:53:26.967Z
Answers.LastActivityDate: 2021-07-03T09:26:57.783Z
Answers.LastEditDate: 2021-07-03T09:26:57.783Z
Answers.UserDisplayName: Stephan
Body: <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>
  
Tags: <bowtie2>
Title: How to export summary data from Bowtie2 for MultiQC to read?
ThreadText: # 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
  
  
  ---
  
  ## 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'
  
  ```
  
  
  ---
  
  