To quantify alterantive splicing events we used Whippet through the downstream module provided by MicroExonator. For additional details of MicroExonator's scRNA-seq module see its documentation page.
We use MicroExonator's scRNA-seq module to perform pairwise comparisons between cell clusters and to obtain a PSI matrix for further downstream analyses.
Neccesary files for this module can be found in the Build folder. We used the following command to perform these comparisons:
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 snakepool
The same files as for the previous module are required, except the config.yaml which can be found at the Build folder. We used the following command to obtain this PSI matrix:
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 merge_quant_by_cluster_PSI