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Old 11-17-2010, 11:47 AM   #1
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Join Date: Aug 2010
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Default Info about rf vs fr with samtools or other?

I am working with Illumina GAII derived mate pair data. I am attempting to identify two things in the sequences so that I can get rid of spurious data:

1. Are the reads rf or fr. I know picard must have the ability to identify this info from a sam as it provides such output when running the ColleceInsertSize... However, the output format is not what I need. Is there another tool that can provide rf/fr data for reads or is there a way to extract it from the sam?

2. Chimeric sequences. Not even sure where to begin here.
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