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Old 07-10-2017, 08:43 AM   #3
horvathdp
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Location: Fargo

Join Date: Dec 2011
Posts: 64
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Hi All (and particularly Brian Bushnell),
I am trying to estimate the genome size of my leafy spurge genome with BBMAP. The ouput says my genome size is a haploid of ~950MB. However, using a procedure described for Jellyfish kmer counts – (sum of (kmer count* the number of kmers))/the peak fold I get 4.6 Gb. The flow cytometry data we have for leafy spurge is 2.1Gb for the 1x genome. From the discussion above, it seems that the BBMAP program measures area under the curve for each peak to get it’s genome size estimate. Given the additional data from the flow cytometry results, I am inclined to believe the method described for the Jellyfish data, but I was wondering why the two methods give such different results, and if there was any reason to prefer the BBMAP method.
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