View Single Post
Old 04-11-2019, 06:12 AM   #104
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978
Default

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.
GenoMax is offline   Reply With Quote