<p>Hello folks!</p>

<p>I want to mask a genome with a particular repeat library using RepeatMasker.</p>

<p>Then I want to cross the coordinates of the repeats with those of gene annotations to find overlaps between them and study associations and stuff.</p>

<p>I&#39;m only starting to consider feasible ways to do that so any input would be great.</p>

<p>Thanks!</p>

<p>The answer by Jon is a good one to get overlaps, and I can tell you how to make the GFF. In the &#39;util&#39; directory of the RepeatMasker distribution there is a script called &#39;rmOutToGFF3.pl&#39; that will do the conversion. The usage is pretty simple since it writes to stdout:</p>

<pre>
perl rmOutToGFF3.pl my_repeatmasker.out &gt; my_repeatmasker.gff</pre>
