Whippet 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
These are the default parameters set in the src/whippet/ENTRYPOINT.sh script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the Whippet manual.
Reference genome in fasta format.--fasta $fasta
The path to the gene annotation file in GTF format for annotation of fusion junctions.--gtf $gtf
Name of bamfile.--bam $controlfolder/*filename*.bam
Output directory for whippet index.-x $outdir/*bamfilename*/graph
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