In addition to the transcriptome assembly discussed, we ran MicroExonator to identify short unannotated exons. Install instructions and general information can be found at MicroExonator's documentation page. Since MicroExonator is still in active development, you can access the specific version we used for this project by accessing a branch called joe with the following command:
git checkout joe
Current versions may produce similar results, but the configuration files needed will be slighly different to the one provided here.
Similarly to the transcriptome assembly analyses, MicroExonator relies on several configuration and data files to run. We ran the Discovery module using the files that can be found at the Build folder. The following command was used to execute the analysis:
snakemake -s MicroExonator.skm --cluster-config cluster.json --cluster "bsub -n {cluster.nCPUs} -R {cluster.resources} -c {cluster.tCPU} -G {cluster.Group} -q {cluster.queue} -o {cluster.output} -e {cluster.error} -M {cluster.memory}" --use-conda -k -j 2000 Report/out.high_quality.txt