Aspli can be used to calculate differential splicing as well as only alternative-splicing events.
If you want to perform differential analysis set
differential=1 in the /scripts/asevent_config.sh config file.Otherwise set
Aspli is an R package. Therefore our ENTRYPOINT.sh script for Aspli calls an R script to run the tool. The parameters listed here are the parameters given to the R script.
These are the default parameters set in the src/aspli/ENTRYPOINT.sh script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the Aspli manual.
The path to the gene annotation file in GTF format for annotation of fusion junctions.--gtf $gtf
Number of threads to be used during the computation--cores $ncores
Length of reads.--readLength $read_length
Output directory. The output will be separated into case and control folder based on the basefolder of the according bam file. If you are running the DICAST pipeline to compare different mapping tools this will include the name of the mapping tool of the used bam file.--out $outdir
1 to run differential analysis, 0 otherwise.--differential $differential