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Old 04-11-2019, 06:12 AM   #104
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Join Date: Feb 2008
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I think you should follow the order of tools that Brian has in his script example. Do clumpify job first. Since you are merging the reads first I am going to speculate that clumpify is unable to identify duplicates properly. If your data in not from a patterned flowcell you could remove the "optical" flag for clumpify.
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