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Bonus exercise: Using Metaxa2 to investigate the taxonomic content
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Now when we are familiar to using R, we can just as well use it to go through
another type of output generated by the Metaxa2 software. Metaxa2 does
classification of rRNA at different taxonomic levels, assigning each read to
a taxonomic affiliation only if it is reliably able to (given conservation
between taxa etc.) You can read more about Metaxa2 here:
http://microbiology.se/software/metaxa2
Install Metaxa2
===============
For this exercise to work, you need Metaxa2 installed. If you did not do this
earlier, here are the installation instructions again. If you did install
Metaxa2 at the beginning of the workshop, you can skip this step and move
straight to the next heading!
The code for Metaxa2 is available from http://microbiology.se/sw/Metaxa2_2.0rc3.tar.gz
You can install Metaxa2 as follows::
# Create a src and a bin directory
mkdir -p ~/src
mkdir -p ~/bin
# Go to the source directory and download the Metaxa2 tarball
cd ~/src
wget http://microbiology.se/sw/Metaxa2_2.0rc3.tar.gz
tar -xzvf Metaxa2_2.0rc3.tar.gz
cd Metaxa2_2.0rc3
# Run the installation script
./install_metaxa2
# Try to run Metaxa2 (this should bring up the main options for the software)
metaxa2 -h
If this did not work, you can try this manual approach::
cd ~/src/Metaxa2_2.0rc3
cp -r metaxa2* ~/bin/
# Then try to run Metaxa2 again
metaxa2 -h
If this brings up the help message, you are all set!
Generating family level taxonomic counts
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If you have already run Metaxa2 to get the number of 16S rRNA sequences,
you can use the output of those runs. Otherwise you need to run the
following command on all the raw read data from all libraries::
metaxa2 -i -o