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?