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Old 02-18-2013, 09:38 PM   #3
me_myself_andI
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Location: Singapore

Join Date: Nov 2010
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I would second the downsampling approach.

The removal of duplicates can in theory and depending on your setup introduce some biases. For example if your looking at subpopulations in viral or bacterial sequencing (i.e. not a 'simple' diploid genome) you might end up with only a handful of reads after duplicate removal, and those will not represent the actual 'allele' frequencies.
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