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Old 07-05-2012, 03:46 AM   #1
plantae
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Location: china

Join Date: Dec 2010
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Default estimate genome size through kmer analysis

hi, all

I have try to use the formula below to estimate genome sizes:

Coverage=(peak k-mer)ŚL/(L-K+1)

Genome size=total_bases/Coverage

But for some dataset, I got several duplication reads, should I exclude these duplicated reads from the dataset before kmer analysis?

The genome contain more than 70% repeats, at 100X depths, how much duplication reads would be expected?
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