Difference between revisions of "GeneMark-EX 2016"
From HPC users
Jump to navigationJump to search
Schwietzer (talk | contribs) (Created page with "== Introduction == GeneMark-EX is a bundled installation of GeneMark-ES and GeneMark-ET. == Installed version == The GeneMark bundle is installed on the environment ''hpc-e...") |
Schwietzer (talk | contribs) |
||
| Line 25: | Line 25: | ||
== 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]. | ||
Revision as of 10:30, 1 October 2018
Introduction
GeneMark-EX is a bundled installation of GeneMark-ES and GeneMark-ET.
Installed version
The GeneMark bundle is installed on the environment hpc-env/6.4: Genemark-EX/4.33-intel-2018a-Perl-5.26.0
Using GeneMark-EX on the HPC cluster
To load GeneMark-EX type in:
module load hpc-env/6.4 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.
