text: user12219: I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I cat the file I get what seem to me to be binary syntax but not sure?
  
  However when I cat into the other pair-end the output seems fine
  
  Any help/suggestion/solution would be greatly appreciated.
  It does seem to be compressed with a missing suffix:
  file pair1.fastq
     pair1.fastq: data.
  
  
  user57: This indeed looks like some sort of binary file. I have seen bunch of those when people renamed .fastq.gz to .fastq without actually uncompressing them. However, as you say, this is not your case, as file pair1.fastq would identify the file as gzip compressed data.
  Looking at possible return values of file comments here, data basically mean the command could not figure out anything about it beside being some sort of binary data file, but I suspect it probably somehow broken file. Honestly, at this point I think you should check the source of the data. If it's from a public database, re-download the data. If it's your own sequencing, contact the sequencing provider and check the data with them. I don't see any way to rescue this file (which does not necerasrily mean there is nothing you can do).
  
original_text: 12219: <p>I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I <code>cat</code> the file I get what seem to me to be binary syntax but not sure?</p>
  <p><a href="https://i.stack.imgur.com/CvKUz.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/CvKUz.png" alt="weird output" /></a></p>
  <p>However when I <code>cat</code> into the other pair-end the output seems fine</p>
  <p><a href="https://i.stack.imgur.com/N9ouH.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/N9ouH.png" alt="correct output" /></a></p>
  <p>Any help/suggestion/solution would be greatly appreciated.</p>
  <p>It does seem to be compressed with a missing suffix:</p>
  <pre><code>file pair1.fastq
     pair1.fastq: data.
  </code></pre>
   57: <p>This indeed looks like some sort of binary file. I have seen bunch of those when people renamed <code>.fastq.gz</code> to <code>.fastq</code> without actually uncompressing them. However, as you say, this is not your case, as <code>file pair1.fastq</code> would identify the file as <code>gzip compressed data</code>.</p>
  <p>Looking at possible return values of <code>file</code> comments <a href="https://unix.stackexchange.com/questions/151008/linux-file-command-classifying-files">here</a>, <code>data</code> basically mean the command could not figure out anything about it beside being some sort of binary data file, but I suspect it probably somehow broken file. Honestly, at this point I think you should check the source of the data. If it's from a public database, re-download the data. If it's your own sequencing, contact the sequencing provider and check the data with them. I don't see any way to rescue this file (which does not necerasrily mean there is nothing you can do).</p>
  