GeneMark-EX 2016

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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.

Installed version

The GeneMark bundle is installed on the environment hpc-env/6.4:

  • Genemark-EX/4.33-intel-2018a-Perl-5.26.0

... and on environment hpc-env/8.3:

  • GeneMark-EX/4.69-GCCcore-8.3.0

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: --ES --sequence seq.fna --ES  --fungi --sequence seq.fna    

To run GeneMark-ET, provide i/genomic sequence and ii/ RNA-Seq read mapped intron coordinates in GFF format: --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.