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Old 07-15-2008, 01:32 AM   #3
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Location: Boston

Join Date: Feb 2008
Posts: 693

This may be caused by PCR duplicates. You should ask wet-lab people to include sufficient large number of molecules before PCR. You can remove PCR duplicates with paired end reads.

Duplicates may also be caused by overlapping clusters. You can tell this from the coordinate of a read on the image.

Fragile region is an alternative cause, but to my experience, this is not the leading cause at least on resequencing.
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