GeneMark-EX 2016

Introduction

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:

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.

Documentation

If you need more information about GeneMark, you can visit their website.