RNA-STAR is a powerful and fast RNA sequence aligner which is designed to align spliced RNA transcripts to a reference sequence.

Using RNA-STAR on RCC Resources

RNA-STAR is available on both Spear and the HPC. The program requires the gnu module to run. After loading this module, you can then run the program using the command STAR (all capital letters). Detailed usage information for RNA-STAR can be found here.  

The following is an example run of the program:

$ module load gnu
# Replace [OPTIONS] with any switches or options needed
# Replace INFILE with the name of the FASTQ files you want to run
# Replace INDEX with a path to a reference genome
$ STAR [OPTIONS] --genomeDir INDEX --readFilesIn INFILE