LINE-1 expression in RNA-Seq data

[rdali094]

Hello,

I have RNA-Seq data and I wanted to look at the expression levels of LINE-1 repetitive elements in this data set. I could not find any LINE elements in the cufflink/cuffdiff report.
Do LINE elements align to the genome using Tophat or are they part of the reads that are lost?

I have read a couple of papers that have looked at the expression level of LINE-1 in their RNA-Seq but their methods were not explained in details.

I am specifically interested in the subset of LINE elements that are active and thus have their promoter in tact.

Ideas?

Thanks!