<p>Hello, </p>

<p>I would like to check whether L1 repetitive elements are modulated between my treatment and control via RNA-Seq. I have read several papers that have done so but their methods are not clear enough for me as a biologist to reproduce. I have analyzed my data using the Tuxedo suite and have analyzed the "unique" genes. I am wondering what modifications have to be taken into account to accommodate the repetitive nature of LINEs. 
1- I have an understanding that some aligners filter out reads that map to several places in the genome. Are my LINE reads being filtered out by tophat?
2- If so, how do I align them? 
3- when using cufflinks, intead of using RefSeq, I am assuming I would have to use a repetitive element model? </p>

<p>Thank you!</p>

You might get some ideas from a solution described in a paper from Peter Park's lab, <a href="http://genomebiology.com/2010/11/6/R69">Estimating enrichment of repetitive elements from high-throughput sequence data</a> which has an online tool available, with source code (<a href="http://compbio.med.harvard.edu/repeats/">Repeat Enrichment Estimator</a>). It appears to be for ChIP-seq though; not sure how adaptable it would be for RNA-seq.

Edit on Apr 27 2015:

I recently had to revisit this problem and found a useful tool that didn't exist at the time of the original answer:

RepEnrich (<a href="http://www.biomedcentral.com/1471-2164/15/583">paper</a>, <a href="https://github.com/nerettilab/RepEnrich">github</a>)