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:
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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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