Difference between revisions of "GeneMark-EX 2016"
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== Introduction == | == Introduction == | ||
GeneMark-EX is a bundled installation of GeneMark-ES and GeneMark-ET. | 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 2016 | BRAKER2]], which we also prvide and might be worth looking into for GeneMark users. | |||
== Installed version == | == Installed version == | ||
The GeneMark bundle is installed on the environment ''hpc-env/6.4: | The GeneMark bundle is installed on the environment ''hpc-env/6.4: | ||
'''Genemark-EX/4.33-intel-2018a-Perl-5.26.0''' | |||
*'''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== | == Using GeneMark-EX on the HPC cluster== | ||
| Line 12: | Line 19: | ||
module load Genemark-EX | module load Genemark-EX | ||
''... or on hpc-env/8.3:'' | |||
module load hpc-env/8.3 | |||
module load GeneMark-EX | |||
''To run GeneMark-ES:'' | ''To run GeneMark-ES:'' | ||
| Line 25: | Line 35: | ||
== Documentation == | == Documentation == | ||
If you need more information about GeneMark, you can visit | If you need more information about GeneMark, you can visit their [http://exon.gatech.edu/GeneMark/background.html website]. | ||
Latest revision as of 13:26, 22 February 2022
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.
