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