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.rousselin@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.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.frwrote:
**
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
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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;