star

Summary

• Module Name: star

• Support Level: Primary Support

• Software Access Level: Open Access

• Home Page: https://github.com/alexdobin/STAR

Software Description

Spliced Transcripts Alignment to a Reference (STAR) is a software package developed for aligning large RNA-seq datasets.

General Linux

To load this module for use in a Linux environment, you can run the command:

module load star

Depending on where you are working, there may be more than one version of star available. To see which modules are available for loading you can run:

module avail star

Slurm Example

#!/bin/bash
#SBATCH --job-name="rfm_RunSTARTest_job"
#SBATCH --ntasks=24
#SBATCH --ntasks-per-node=24
#SBATCH --output=rfm_RunSTARTest_job.out
#SBATCH --error=rfm_RunSTARTest_job.err
#SBATCH --time=0:10:0
#SBATCH -p msismall
module load star/2.5.3a
wget https://public.s3.msi.umn.edu/reframe/sw/star/Melampsora_laricipopulina....
wget https://public.s3.msi.umn.edu/reframe/sw/trimmomatic/seq.fq
STAR --runMode genomeGenerate --runThreadN 24 --genomeDir ./ --genomeFastaFiles Melampsora_laricipopulina.GCA_000204055.1.dna.toplevel.fa
STAR --genomeDir ./ --runThreadN 24 --readFilesIn seq.fq --outFileNamePrefix output