STAR
From ScientificComputing
Please note that this application page is referring to the old CentOS software stack which is obsolete and does not work any more with the new Ubuntu setup. You can find an overview on the Ubuntu software stack on this wiki page.
Contents
Category
Bioinformatics, AlignerDescription
STAR is an alignment tool for RNA-seq, developed by Alexander Dobin et al. STAR is implemented as a standalone C++ code.Available versions (Euler, old software stack)
| Legacy versions | Supported versions | New versions |
|---|---|---|
| 2.4.2a, 2.5.3a |
Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.
Environment modules (Euler, old software stack)
| Version | Module load command | Additional modules loaded automatically |
|---|---|---|
| 2.4.2a | module load gcc/4.8.2 star/2.4.2a | |
| 2.5.3a | module load gcc/4.8.2 star/2.5.3a |
Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.
How to submit a job
You can submit a STAR job in batch mode with the following command:sbatch [Slurm options] --wrap="STAR [STAR options]"Here you need to replace [STAR options] with STAR command line options (please have a look at the STAR manual for getting a list of all command line options) and [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system.
