Quantifying copies of a single locus

[robinweide]

Hi all,

I'm trying to count to number of repeating elements in a genome (the locus of interest has a variable number of copies). Trying to keep it simple has led me to count mapped NGS-reads to an custom "reference", containing the repeating element and some control-loci/genes (actin, etc) as separate chromosomes. From this, I want to compare the ratio (reads mapped to the loci/reads mapped to control) between different samples.

Is this valid or must I do this analysis on the whole genome? Wat kind of statistics do you recommend?

Thanks