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:
- bedtools using a reference bed file from repbase/UCSC browser then a simple barplot of overlap.
- IGV after alignment to hg19 then inspecting regions with large pileups.
- 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?