[BioC] insertion site detection

[Wei Shi]

Dear Alpesh,

Not sure if this will help, but the Subread aligner in Rsubread package can detect ~200bp insertions.

Cheers,
Wei

On Sep 9, 2014, at 3:13 PM, Alpesh Querer wrote:

> 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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> 
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