HPC:STAR

STAR

STAR is an ultrafast universal RNA-seq aligner. Currently, there are two versions of the STAR aligner installed on the PMACS HPC cluster. HG19 and MM9 genome indexes for the older version of STAR is also available on the cluster.

Note: The available hg19 and mm9 STAR genome indexes are incompatible with the newer version of STAR, v2.4.1d. It is not recommended to use these indexes if you wish to use version of the STAR aligner.

Usage

To check what each of modules are doing:


[asrini@node061 ~]$ module show STAR-2.3.0e 
-------------------------------------------------------------------
/usr/share/Modules/modulefiles/STAR-2.3.0e:

module-whatis	 STAR: An ultrafast universal RNA-seq aligner 
prepend-path	 PATH /opt/software/STAR/2.3.0e/bin 
prepend-path	 PERL5LIB /opt/software/STAR/2.3.0e/STAR-Fusion-0.1.1/lib 
-------------------------------------------------------------------

[asrini@node061 ~]$ module show STAR-mm9 
-------------------------------------------------------------------
/usr/share/Modules/modulefiles/STAR-mm9:

module-whatis	 STAR: aligns RNA-seq reads; This module file sets up the GENOME_DIR environment variable to pass to STAR executable's --genomeDir flag 
setenv		 GENOME_DIR /home/apps/STAR/indexes/mm9 
-------------------------------------------------------------------


[asrini@node061 ~]$ module show STAR-hg19 
-------------------------------------------------------------------
/usr/share/Modules/modulefiles/STAR-hg19:

module-whatis	 STAR: aligns RNA-seq reads; This module file sets up the GENOME_DIR environment variable to pass to STAR executable's --genomeDir flag 
setenv		 GENOME_DIR /home/apps/STAR/indexes/hg19 
-------------------------------------------------------------------

[asrini@node061 ~]$ module show STAR-2.4.1d 
-------------------------------------------------------------------
/usr/share/Modules/modulefiles/STAR-2.4.1d:

module-whatis	 STAR: An ultrafast universal RNA-seq aligner 
prepend-path	 PATH /opt/software/STAR/2.4.1d/bin 
prepend-path	 PERL5LIB /opt/software/STAR/2.4.1d/STAR-Fusion-0.1.1/lib 
-------------------------------------------------------------------

Load the STAR-2.3.1e module:

[asrini@node061 ~]$ module load STAR-2.3.0e 

[asrini@node061 ~]$ which STAR
/opt/software/STAR/2.3.0e/bin/STAR

Using an available STAR index:

[asrini@node061 ~]$ module load STAR-hg19 

[asrini@node061 ~]$ echo $GENOME_DIR 
/home/apps/STAR/indexes/hg19

Once loaded, you can then use the system provided index by passing $GENOME_DIR to STAR's --genomeDir option :

STAR --genomeDir $GENOME_DIR

HPC:STAR

STAR

Usage

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