STAR
STAR is an ultrafast universal RNA-seq aligner. Currently, there are multiple 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 STAR v2.4.1d or newer. 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 (recommended only with STAR v2.3.0e):
[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
