<p>As part of their submission requirements ENA/ArrayExpress require BAMs to include all reads (e.g. also unmapped ones). TopHat in its wisdom splits unmapped reads from the accepted_hits.bam output.</p>

<p>However, creating a &#39;complete&#39; BAM is not so straightforward due to problems in the unmapped reads BAM (detailed on <a href="http://seqanswers.com/forums/showthread.php?t=28155">seqanswers</a>). I&#39;ve tried the script mention on SeqAnswers, but it doesn&#39;t solve all the problems for me. I still get unmapped reads which don&#39;t have a mate in accepted_hits.bam</p>

<p>Given TopHat&#39;s popularity this should be a solved problem, right? So, how does everyone deposit their TopHat alignments for publication? Or are fastqs the preferred format.</p>

<p>Any suggestions?</p>

With the help of Christian Brueffer, I managed to resolve this problem. See his github: https://github.com/cbrueffer/tophat-recondition/issues/1#issuecomment-129849801