Star
Description
Application STAR (Spliced Transcripts Alignment to a Reference) can by used for the detection and characterization of sliced RNAs.
License
STAR is a free open source software distributed under GPLv3.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of star and load default version of star as
module avail star/ # list available modules module load star # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail star
and choose explicit version you want to use. Example of module initialization and run:
$ module add star-2.4.1b
$ STAR --option1 value1 --option2 value2
The application supports parallel computing. For this reason the important option is --runThreadN. This option the defines the number of threads to be used for genome generation. By default it is 1. Other parameters are described in the STAR manual.
It is appropriate to set the number of threads to value of the variable PBS_NUM_PPN:
STAR --runThread $PBS_NUM_PPN ...
Documentation
- Online documentation STAR manual.
- Paper about the application and used algorithms: STAR: ultrafast universal RNA-seq aligner
- Forum/author's support