insertion site detection

Hi all,

I need your guidance in this, I have dna sequence paired end reads with
 known non-reference transposable element sequence insertions (~1000 bp). I
do have a reference genome. I am wondering if there are bioconductor
packages, and/or other software that can help me identify the insertion
sites. I would also like to pick your brains on how to go about doing this,
what is the optimal protocol that is.

Thanks a lot for your help,

Al

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