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Old 03-25-2010, 05:28 AM   #21
MattB
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Location: Norway

Join Date: Aug 2008
Posts: 35
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Good points there. In our case, we were not too concerned about rare alleles, in fact we planned to avoid those SNPs!

I don't think I've really mentioned it above, but in our case the goal was to find 3000 or so polymorphic SNPs throughout the genome for subsequent genotyping in a linkage mapping study. Therefore, the strategy I describe is related to this goal:

-20 individuals represented the subsequent mapping population
-transcriptome sequencing gave us good depth and some annotation info
-pooling enabled us to run only 2 lanes for cost efficiency

All these things probably need to be modified like lletourn suggests if you have different goals in mind.
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