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Old 06-10-2011, 09:16 AM   #21
Location: USA

Join Date: Apr 2010
Posts: 76
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UPDATE June 10, 2011: I contacted Illumina and they were confused too. However, finally they (and people at TopHat and our sequencing center) resolved the issue. The reads that come out of the machine have the same sequence as the CODING strand of the DNA and not the template strand.

The correct option to use for Cufflinks is fr-secondstrand
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