TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
To see what versions of TopHat are available type
module avail tophat
To see what other modules are needed, what commands are available and how to get additional help type
module help tophat
To use TopHat, include a command like this in your batch script to load the TopHat module:
module load tophat
Be sure you also load any other modules needed, as listed by the
module help tophat command.