Star

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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

Homepage

https://github.com/alexdobin/STAR