EventPointer

Note

EventPointer 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.

EventPointer Factsheet

Toolname	eventpointer
Version	2.4.0
License	Artistic software License 2

Required Files

• gtf , bam

Links

• EventPointer manual

• EventPointer publication: EventPointer: an effective identification of alternative splicing events using junction arrays

Note

EventPointer is an R package. Therefore our ENTRYPOINT.sh script for EventPointer calls an R script to run the tool. The parameters listed here are the parameters given to the R script.

Parameters

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

--gtf

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

--gtf $gtf

--cores

Number of threads to be used during the computation

--cores $ncores

--out

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

--bamfolder

Location of bam files.

--bamfolder $controlfolder

--differential

1 to run differential analysis, 0 otherwise.

--differential $differential