Software Category


STAR is a genomic sequence data alignment program which aligns RNA-seq transcript sequence data to reference transcripts. The program is designed to be extremely fast and accurate at performing these types of alignments. For more information, please refer to the main website.

Using STAR on RCC Resources

On RCC resources, STAR requires the gnu module to be loaded in order to be used. The basic format for using STAR from the command line is STAR --[OPTIONS]. In the list of options, you have to specify both the options and the option values. Included in this list will be paths to the locations of genome files you want to use STAR with. For detailed usage documentation, refer to the STAR manual.

    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