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”