Whippet

Note

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 differential=0.

Whippet Factsheet

Toolname	whippet
Version	0.11.1
License	MIT Licence

Required Files

• fastq , fasta , gtf

Links

• Whippet manual

• Whippet publication: Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop

Parameters

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.

--fasta

Reference genome in fasta format.

--fasta $fasta

--gtf

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

--gtf $gtf

--bam

Name of bamfile.

--bam $controlfolder/*filename*.bam

-x

Output directory for whippet index.

-x $outdir/*bamfilename*/graph

-o

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