STAR aligner

Spliced Transcripts Alignment to a Reference is a fast RNA-seq read mapper, with support for splice-junction and fusion read detection.

Documentation

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. . Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635

Usage on Bridges-2

To see what versions of STAR are available and if there is more than one, which is the default, along with some help, type

module spider STAR

To use STAR, include a command like this in your batch script or interactive session to load the STAR module: (note ‘module load’ is case-sensitive):

module load STAR

Usage on Bridges

To see what versions of STAR aligner are available type

module avail staraligner

To see what other modules are needed, what commands are available and how to get additional help type

module help staraligner

To use STAR aligner, include a command like this in your batch script or interactive session to load the staraligner module:

module load staraligner

Be sure you also load any other modules needed, as listed by the module help staraligner command.