STAR¶
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.
Usage¶
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:
#!/bin/bash
#SBATCH -n 2 # (or --ntasks=2) Request 2 cores
#SBATCH --mem-per-cpu=2G # Request 2GB RAM per core
#SBATCH -t 1:0:0 # Request 1 hour runtime
module load star
# Genome indexing
STAR --runMode genomeGenerate \
--genomeDir <input_fasta_dir> \
--genomeFastaFiles <input_fasta> \
--runThreadN ${SLURM_NTASKS}
# Genome alignment
STAR --runMode alignReads \
--genomeDir <input_fasta_dir> \
--readFilesIn <input_file(s)> \
--runThreadN ${SLURM_NTASKS}