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Old 06-10-2011, 09:09 AM   #3
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Join Date: Jun 2011
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Originally Posted by ETHANol View Post
This is a wild guess but I would bet it has to be one of two things: 1) biases generated during PCR amplification of your library. Perhaps the GC content is different near the ends of the chromosomes. Or 2) The ends of the chromosomes fragment more efficiently.
Hmm, good idea...if there were subtle differences in the setup of individual PCRs, or in the fragmentation step for each sample, then the biases you mention could be showing up in some samples but not others. Thanks for your help!
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