Hi Antoine.
Thanks - sorry, I haven't analysed that particular platform - anyone?

http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics
seems comprehensive...
Why not try the Galaxy picard Hybrid Selection metrics tool on your data?

On Wed, Dec 21, 2011 at 6:25 PM, Antoine ROUSSELIN
<a.rousse...@baclesse.fr> wrote:
>
> Hello,
>
> My English is very bad, it's a shame!
>
> My I have a file for my baits (create a bed file of your Agilent SureSelect 
> targets with exons and introns captured). Sequencing output, I get the files. 
> Bam, my result sets of alignments on the human genome complete (with CASAVA). 
> I try to get the coverage I only exonic regions (+ or - 50 bp).
>
> Thanks
>
> ROUSSELIN Antoine
> Clinical Biology and Oncology Laboratory
> Centre François BACLESSE
> France/Caen
> a.rousse...@baclesse.fr
> Tel : (33) 02.31.45.40.44
> Fax : (33) 02.31.45.50.53
>
>
>
> -------- Message d'origine--------
> De: Ross [mailto:ross.laza...@gmail.com]
> Date: mer. 12/21/2011 03:16
> À: Antoine ROUSSELIN
> Cc: galaxy-user@lists.bx.psu.edu
> Objet : Re: [galaxy-user] % On-Off target
>
> Hello Antoine,
> I'm not sure I really understand your question but if the metrics described
> at http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics are
> of use, you could try the picard hybrid selection metrics Galaxy tool or
> use it on the command line. Otherwise perhaps you can get a more helpful
> response if you provide a clear explanation of the data formats you have
> and the measures you want.
>
>
> On Wed, Dec 21, 2011 at 2:59 AM, Antoine ROUSSELIN
> <a.rousse...@baclesse.fr>wrote:
>
> > **
> >
> > hello,
> > I'm looking for a tool (or command line) to determine the % On-Off target
> > + or - 50 bp of exon from my capture file but not annotated (!!!). Capture
> > SureSelect agilent home.
> >
> > Current pipeline:
> > GAIIx Illumina
> > CASAVA1.8
> > IGV
> > CNV-seq
> > SAMtools
> > BEDtools
> > GALAXY
> > NextGENe
> >
> > Please HELP
> >
> > ROUSSELIN Antoine
> > Clinical Biology and Oncology Laboratory
> > Centre François BACLESSE
> > France/Caen
> > a.rousse...@baclesse.fr
> > Tel : (33) 02.31.45.40.44
> > Fax : (33) 02.31.45.50.53
> >
> >
> > ___________________________________________________________
> > The Galaxy User list should be used for the discussion of
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> >
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> >
>
>
>
> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>



--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

___________________________________________________________
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