I've been trying to find a way to query fastq files for particular sequence elements. Our data was mapped using BWA by our collaborator, and repetitive elements 'ignored', but we are now interested in determining whether a couple specific repetitive elements of interest are differentially represented in the raw read files. Are there any tools that anyone has developed to do anything like this -- and that perhaps I'm simply missing as I explore the available tools?

In the short term, I've written a very crude python script to begin exploring the question, but I'm sure there has to be a much better way.

If there are no such tools available, I'm hopeful that someone might have some helpful suggestions, or that perhaps it could be explored during the upcoming conference &/or training day in July.