<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>

If I understand your question correctly, you want to identify the expression levels of of LINE-1 repeats in your RNA-Seq samples? If that is the case follow these instructions.

1. Make a GTF format file your repeat elements or download them from UCSC/Galaxy and run
2. `tophat -G LINE1-repeats.gtf -o treat-rnaseq yourgenome_ebwt_base treat-rnaseq.fastq`
3. `tophat -G LINE1-repeats.gtf -o control-rnaseq yourgenome_ebwt_base control-rnaseq.fastq`
4. `cuffdiff -G LINE1-repeats.gtf treat-rnaseq.bam control_rnaseq.bam`

Step 2 and 3 do the map the RNA-Seq reads to your repeat elements in the genome.

Step 4 calculates the differential expression of your repeat elements in your treatment and control.