Parsing output of .cons.tax.summary

Hello,

How do I interpret the output from .cons.tax.summary? I would like to get the seq counts for all for all my samples at the family level. I have used the count file all throughout out so my outputted .cons.tax.summary is equivalent to the MiSEQ SOP tutoiral. I assumed that taxlevel, in the outputted files, corresponded to the 6 tax levels I know of. However, there are a total of 19 taxlevels and I don’t know how to interpret that. I’ve tried to google the taxons to understand it seems that things are a bit all over the place - for example Fungi and a kingdom, but Alveolata are a superphylum and Virdiplantae are a phlyum? I don’t know what to do with this downstream… I was kind hoping that everything with taxlevel rank 2 would represent the same thing (i.e Kingdom, or Phylum).

Does anyone have any suggestions? As I am new to this type of analysis, I’ve stuck with all the default parameters suggested in the MiSeq tuotiral. As you can also tell I am looking at 18S data, I’ve used the silva.eukaya downloads that I got off the MOTHUR site as my input files.

Here’s and example of my output (ignore the rightmost column, that’s just from the R data frame) of just the taxa information.

     taxlevel rankID         taxon daughterlevels
3           2  0.1.1     Alveolata              4
219         2  0.1.2     Amoebozoa              1
237         2  0.1.3   Cryptophyta              3
367         2  0.1.4    Euglenozoa              1
399         2  0.1.5         Fungi              3
792         2  0.1.6       Metazoa              8
1111        2  0.1.7 Viridiplantae              3
1479        2  0.1.8 stramenopiles              5
1640        2  0.1.9  unclassified              1

How do I interpret the output from .cons.tax.summary? I would like to get the seq counts for all for all my samples at the family level. I have used the count file all throughout out so my outputted .cons.tax.summary is equivalent to the MiSEQ SOP tutoiral. I assumed that taxlevel, in the outputted files, corresponded to the 6 tax levels I know of. However, there are a total of 19 taxlevels and I don’t know how to interpret that. I’ve tried to google the taxons to understand it seems that things are a bit all over the place - for example Fungi and a kingdom, but Alveolata are a superphylum and Virdiplantae are a phlyum? I don’t know what to do with this downstream… I was kind hoping that everything with taxlevel rank 2 would represent the same thing (i.e Kingdom, or Phylum).

This is a problem with the eukaryotic taxonomy from SILVA not conforming to the Linnean system that you are anticipating. The summary file is described at http://www.mothur.org/wiki/Classify.seqs

What do folks do to get around this issue? I really need a taxonomy that uses the Linnaean system. Thanks for any suggestions!