Greetings all,

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.

Thanks and Best Regards,  Jane

Jane E. Dorweiler, PhD
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