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. 




Usage on Bridges


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 or interactive session 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.