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Old 02-19-2013, 08:07 AM   #3
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,091

MiSeq has known problems with libraries that have low nucleotide diversity. There are several threads (an example thread: on SeqAnswers that address that issue. There are workarounds proposed but no definite solution as yet.

As for the answers regarding the chemistry used for the 3 platform and the differences search through these FAQ's.
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