Difference between revisions of "GeneMark-EX 2016"
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''... or on hpc-env/8.3:'' | ''... or on hpc-env/8.3:'' | ||
module load hpc-env/8.3 | module load hpc-env/8.3 | ||
module load GeneMark- | module load GeneMark-EX | ||
''To run GeneMark-ES:'' | ''To run GeneMark-ES:'' | ||
Revision as of 13:15, 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.
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-ET/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.
