Plot pileup of reads multiply aligned to repetitive elements

Question

[kevin.stachelek]

I am looking at repetitive elements as a biomarker in cancer. We have identified a few candidate repetitive elements via tetranscripts. I've taken a couple of approaches to visualizing this data:

1. bedtools using a reference bed file from repbase/UCSC browser then a simple barplot of overlap.
2. IGV after alignment to hg19 then inspecting regions with large pileups.
3. IGV after alignment exclusively to the Repetitive element consensus sequence (this feels inappropriate to me).

We want to find out whether a particular region of the repetitive element of interest has higher proportion of aligned reads between disease and control groups.

Is there a common way to visualize a pileup across basically similar genomic regions, so we can identify a 'consensus' sequence in this differentially expressed repetitive element?. Something from multiple sequence alignment tools maybe?

Thanks!