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Old 09-13-2014, 02:49 PM   #1
fhsantanna
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Location: Porto Alegre

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Default NORMALIZED tetranucleotides frequency

I want to do a PCA of metagenomic contigs based on tetranucleotide composition. Commonly I read in the literature the use of NORMALIZED tetranucleotide frequencies for this purpose, however no detail about this normalization is given.

What did they mean about "normalization"? Is it a z-score transformation? Or is it a normalization depending on the length of the contigs (how do I calculate it?)?

Some references:
http://www.nature.com/srep/2011/1110...srep00135.html
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021199/

Thanks.
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binning, contigs, metagenomics, normalization, tetranucleotide

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