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Old 02-09-2017, 11:12 AM   #9
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,014

What setting did you use for dupedist? For a 4000 flowcell data you need to include
dedupe=t optical=t dupedist=2500 dupesubs=0 spantiles=f
to your clumpify command line. (dupesubs=0 will only look for perfectly matching reads without any errors).

If you did not use even one of those options then I suggest that you try again.
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