GeneMark-EX is a bundled installation of GeneMark-ES and GeneMark-ET. This bundle is an eukaryotic gene prediction suite with automatic training.
Also, GeneMark-EX is part of BRAKER2, which we also prvide and might be worth looking into for GeneMark users.
The GeneMark bundle is installed on the environment hpc-env/6.4:
... and on environment hpc-env/8.3:
Using GeneMark-EX on the HPC cluster
To load GeneMark-EX type in:
module load hpc-env/6.4 module load Genemark-EX
... or on hpc-env/8.3:
module load hpc-env/8.3 module load GeneMark-EX
To run GeneMark-ES:
gmes_petap.pl --ES --sequence seq.fna gmes_petap.pl --ES --fungi --sequence seq.fna
To run GeneMark-ET, provide i/genomic sequence and ii/ RNA-Seq read mapped intron coordinates in GFF format:
gmes_petap.pl --sequence seq.fna --ET introns.gff --et_score 4
You should adjust command line parameter "--et_score", depending on the type of RNA-Seq read alignment tool used.
If you need more information about GeneMark, you can visit their website.