Difference between revisions of "GeneMark-EX 2016"

From HPC users
Jump to navigationJump to search
 
(4 intermediate revisions by the same user not shown)
Line 2: Line 2:
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.
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'':
... and on environment ''hpc-env/8.3'':


*'''GeneMark-ET/4.69'''-GCCcore-8.3.0
*'''GeneMark-EX/4.69'''-GCCcore-8.3.0


== Using GeneMark-EX on the HPC cluster==
== Using GeneMark-EX on the HPC cluster==
Line 17: 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:''

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.