title: Using bwa mem and umitools together
body: <p>I am trying to use bwa mem to align sequence reads to the hg19 reference but my sequences all have a UMI (Unique molecular Identifier). I used umitools like so:</p>
  
  <pre><code>umitools trim --end 5 input.fastq NNNNNN &gt; output.fastq
  </code></pre>
  
  <p>This then properly appended my UMI sequence to the name line in the output.fastq file, but then when using bwa mem to align, I get the error that:</p>
  
  <pre><code>paired reads have different names: "someTitle:UMI_ATGCTC", "someTitle:UMI_CATTAT"
  </code></pre>
  
  <p>Is there a way to use both bwa mem and umitools together so this doesn't happen?</p>