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Spliced Transcripts Alignment to a Reference (STAR) is a universal, RNA-seq aligner. In addition to unbiased detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

STAR is available as a module on Apocrita.


To run the default installed version of STAR, simply load the star module:

$ module load star
$ STAR --help

Usage: STAR  [options]... --genomeDir REFERENCE   --readFilesIn R1.fq R2.fq

For full usage documentation, run STAR --help.

Example job

Serial job

Here is an example job running on 2 cores and 4GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load star

# Genome indexing
STAR --runMode genomeGenerate \
     --genomeDir <input_fasta_dir> \
     --genomeFastaFiles <input_fasta> \
     --runThreadN ${NSLOTS}

# Genome alignment
STAR --runMode alignReads \
     --genomeDir <input_fasta_dir> \
     --readFilesIn <input_file(s)> \
     --runThreadN ${NSLOTS}