STAR
STAR (Spliced Transcripts Alignment to a Reference) is a fast NGS read aligner for RNA-seq data.
License
Free to use and open source under GNU GPLv3.
Available
- Roihu: 2.7.11b, via the
bio-appsmodule.
Usage
STAR is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the STAR module:
Before you can run the actual alignment job, you must index your fasta formatted reference genome. On Roihu the working copies of reference genome indexes, as well as any large files, should be stored to the /scratch directory.
For ease of use, set an environment variable to point to your /scratch directory. (Substitute the correct path for the one used in the example.)
Create a directory for the reference genome index:
After that, the indexing can be done with command:
STAR --runMode genomeGenerate --genomeDir $SCRATCH/star-genome --genomeFastaFiles /path/to/genome/genome.fasta --runThreadN 2
Once the indexing is done, the actual mapping task can be launched. STAR will generate the mapping output using fixed file names. Because of that it is recommended that each STAR job is run in a new, empty directory. On Roihu you should create this new job directory to the /scratch directory of your project. A new directory called starjob1 can be created with command:
after that the actual mapping job can be launched with commands:
The default parameters STAR uses are typical for mapping 2x76 or 2x101 Illumina reads to the human genome.
On Roihu, all computing tasks should be executed as batch jobs. In batch jobs you can also utilize thread based parallelization. Below is a sample batch job file for STAR. The job uses six computing cores from a single computing node. The memory reservation is 24 GB. Note that you must change the --account setting to match your project.
#!/bin/bash
#SBATCH --job-name=STAR
#SBATCH --account=<project>
#SBATCH --output=STAR.stdout
#SBATCH --error=STAR.stderr
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --mem=24000
module load bio-apps/v202603
module load star/2.7.11b
export SCRATCH=/scratch/<project>/$USER
# calculate indexes. You don't need to recalculate the indexes if they already exist.
mkdir $SCRATCH/star-genome
STAR --runMode genomeGenerate --genomeDir $SCRATCH/star-genome --genomeFastaFiles /path/to/genome/genome.fasta --runThreadN $SLURM_CPUS_PER_TASK
# Run the mapping task
STAR --genomeDir $SCRATCH/star-genome --readFilesIn my-reads.fastq --runThreadN $SLURM_CPUS_PER_TASK
The batch job script is launched with command sbatch. For example: