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.rousselin@baclesse.fr
Tel : (33) 02.31.45.40.44
Fax : (33) 02.31.45.50.53



-------- Message d'origine--------
De: Ross [mailto:ross.lazarus@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.rousselin@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.rousselin@baclesse.fr
> Tel : (33) 02.31.45.40.44
> Fax : (33) 02.31.45.50.53
>
>
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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;