MAJIQ

Note

MAJIQ 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.

Parameters

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

build reference

The path to the gene annotation file in GFF format.

$gff
-c

MAJIQ config file (built based on DICAST config parameters in ENTRYPOINT.sh)

-c $config
-j

Number of threads to be used during the computation

-j $ncores
-o

Output directory with majiq build output.

-o $outdir/$outdir_name/build
maqiq psi

Run MAJIQ in psi mode with files built from gff as input.

-j

Number of threads to be used during the computation

-j $ncores
-o

Output directory with psi output. Used to build splicegraph with voila.

-o $outdir/$outdir_name/psi
-n

Run with bam files as input.

-n “BAM”