text: user12676: 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?
  
  user12676: 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'
  
  
original_text: 12676: <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>
   12676: <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>
  