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A program for ultrafast RNA-seq sequence alignments

STAR requires an environment module

In order to use STAR, you must first load the appropriate environment module:

module load gnu

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.

Using STAR on the HPC#

The basic format for using STAR from the command line is STAR --[OPTIONS]. In the list of options, you have to specify both the option name and the corresponding option value. This list should include the paths to the locations of the genome files you want to use STAR with.

Below is a short example of using STAR with the genomeDir and readFilesIn options.

 $ module load gnu

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