UniFrac: Taxa specific and Abundance Weighted

Today I’ve been working on a LOT of UniFrac data.

First off, on the Metagenetics95A_mac database, I added the following amendments to taxa info:

  • Unicellular Eukaryotes all marked with ‘Unicellular’ in the phosphate_slv field
  • Enoplids all marked with ‘Enoplida’ in the phosphate_slv field
  • All nematodes marked with ‘Nematode’ in the remark field

Abundance weighting–Did this in two ways:

  1. Stringent–Just converted the sequence reads in each sample into percentages, rounded these numbers off using the cell formatting options (show 0 decimal places).  This actually cut out a lot of taxa since many had percentages <0 but were converted into ‘no sequence reads’ when the percentages were rounded.
  2. My Modification (files labelled My Mod)–I doubled the values (percentages) of taxa who had interger values (1 and above) when the percentages were rounded under ‘stringent’ parameters.  Taxa who had reads but were showing up as zero were iterated as ‘1’, to signify that this taxa was present but at minimal values.
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