code: def _prepare_file(fn, out_dir):
      
      atropos = _get_atropos()
      cmd = "{atropos} trim --max-reads 500000 -u 22 -se {fn} -o {tx_file}"
      out_file = os.path.join(out_dir, append_stem(os.path.basename(fn), "end"))
      if file_exists(out_file):
          return out_file
      with file_transaction(out_file) as tx_file:
          do.run(cmd.format(**locals()))
      return out_file
docs: Cut the beginning of the reads to avoid detection of miRNAs