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Old 07-06-2011, 08:03 AM   #3
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Could be from the Ampure beads remaining in solution? I tend to leave the plate on the magnetic stand for a few minutes more than in the manual (7 vs. 5 minutes). Also check pipet tip carefully to see if any beads remain. Can be hard to take supernatant without taking up some beads. Also are you seeing this in all libraries?

By the way are you doing the standard PCR enrichment (all 15 cycles)? Not seeing the ubiquitous 'bump' ~600-2000bp, wondering why.
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