I have a consensus sequence for a class of repetitive elements (from repbase) and I want to find out the depth coverage of the real genomic instances (taken from ucsc rmask table) against this consensus sequence. The elements tend to become 5' truncated over evolutionary time, so some instances may be quite short, while some instances are full length. I would like to get out something in the end like a wigg file describing the "depth" of instances at each position in the consensus, but I am not sure how to go about it. Any help is greatly appreciated.
One approach I was considering is to break up my instance sequences into k-mers of say 50bp and then align to the consensus reference via bowtie producing BAM and then using samtools to get the windowed coverage. Thoughts?