Editing Nanopore RNA Sequencing Protocol (section)

====m6ANet====

'''m6ANet''' is a new m6A detection method that uses the variance in electrical signal across multiple transcript reads to determine if a base modification is present at a given locus. It requires much fewer pre-requisite software packages than other methods (such as ''EpiNano''), does not require a specific basecaller version, and is much more accurate than other contemporarily available detection methods (such as ''Tombo'').

To install, we want to first make a ''Conda'' environment that is specific to ''m6ANet''. When you install it, it will automatically install a few ''Conda'' packages (like ''pytorch'') and you don’t want any conflicts with your existing packages.

<code>Bash</code>
<syntaxhighlight lang="Bash">
conda create --name m6anet
conda activate --stack m6anet
</syntaxhighlight>

Next, move into the default directory where you want to store the ''m6ANet'' folder. Then, pull ''m6ANet'' from GitHub and install via the following (alternatively, you can do this using <code>pip</code> by executing <code>pip install m6anet</code>):

<code>Bash</code>
<syntaxhighlight lang="Bash">
git clone "https://github.com/GoekeLab/m6anet.git"
cd m6anet
python setup.py install
</syntaxhighlight>

You should now have ''m6ANet'' installed and ready to go. As with all of the other installations, '''''make sure you pay close attention''''' to the console to see if it throws an error during the installation. You may need to manually install or update other packages, like <code>openssl</code>, if it returns an error.