Extension: Comparing OTU methods

Now that we’ve learned a quick method of building trees, we can use this knowledge to compare our OTUs from different methods.

Data

The input data for this extension is two or more FASTA files comprising OTUs generated by different methods. If you’re following along step-by-step, these would have been produced in the OTU delimitation tutorials. Alternatively, you can use the following files from the sectionD archive as example data:

  • Greedy clustering: otus_greedy_0.97.fasta
  • Linkage delimitation: otus_linkage_13.fasta
  • Bayesian clustering: otus_crop_s.fasta
  • Phylogenetic delimitation: otus_bPTP.fasta

First, let’s create a directory for this little side project, just to be organised

Second, we need to create copies of our OTU files with names added to the headers in order to differentiate OTUs from different methods. For each OTU file, run the following command, replacing method with a description of the method used to create OTUS, e.g. greedy97 (text or numbers only, no spaces or other characters!):

sed -e "s/\(^>.*$\)/\1method/" input.fasta > newdirectory/output.fasta

Next, concatenate these OTU files into one file - you’ll need to be inside your new directory for this:

cat *.fasta > output.fasta

Exercise

  • Run FastTree on this file, using the command from the previous tutorial.
  • How do different OTUs match up with the different methods?