<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>

Sounds like a job for [BedTools][1]. You should be able to make a GFF from the RepeatMasker output and use `bedtools intersect` to find overlaps.

 [1]: http://bedtools.readthedocs.org/en/latest/