View source for 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.

== 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 [http://exon.gatech.edu/GeneMark/background.html website].