SplAdder 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 differential=0.


These are the default parameters set in the src/spladder/ENTRYPOINT.sh script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the SplAdder manual.


Name of bamfile.

-b $controlfolder/*filename*.bam

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.

-o $outdir

The path to the gene annotation file in GTF format for annotation of fusion junctions.

-a $gtf

Number of threads to be used during the computation

--parallel $ncores

Length of reads.

-n $read_length

Output in txt format.