% On-Off Target

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Question: % On-Off Target

6.9 years ago by

Antoine ROUSSELIN • 20

Antoine ROUSSELIN • 20 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

samtools bedtools bam • 733 views

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modified 6.9 years ago by fubar ♦ 1.1k • written 6.9 years ago by Antoine ROUSSELIN • 20

6.9 years ago by

fubar ♦ 1.1k

Australia

fubar ♦ 1.1k wrote:

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

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