Editing Nanopore RNA Sequencing Protocol (section)

====Run Inference====

{{tip|M6ANet may run into issues if your shell open file limit is too low. The max number of open files can be viewed with the <code>ulimit -n</code> command. To change this, simply add a number following the command (e.g., <code>ulimit -n 100000</code>).}}

Finally, we can execute the final bit of code to generate the final output:

<code>Bash</code>
<syntaxhighlight lang="Bash">
m6anet-run_inference \
--input_dir $M6AO \
--out_dir $M6AO \
--infer_mod_rate \
--n_processes 4
</syntaxhighlight>

Note that the <code>--input_dir</code> here is the output folder from the previous step that contains your <code>eventalign.index</code> file, <code>data.index</code> file, etc. The <code>--out_dir</code> can be specified as something else, but I wanted to put the output from this last step back into the final folder. The output is a <code>.gz</code> file, which might need to be unzipped via the command line if you have trouble using the GUI to do so:

<code>Bash</code>
<syntaxhighlight lang="Bash">
cd $M6AO
gunzip data.result.csv.gz
mv data.result.csv ${SAMPLEID}_m6anet_result.csv
</syntaxhighlight>