TopHat uses Bowtie, a high-throughput short read aligner, to analyze the mapping results for RNA-Seq reads and identify splice junctions.


Please note that tophat (and bowtie) cannot run in parallel, that is, on multiple nodes.  Submitting multi-node jobs will only waste resources.  In addition you must explicitly include the '-p' option to use multiple threads on a single node.

Availability and Restrictions


TopHat is available on the Owens Cluster. The versions currently available at OSC are:

Version Owens
2.1.1 X*
* Current default version

You can use module spider tophat to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


TopHat is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type, Open source


Usage on Owens


To configure your enviorment for use of TopHat, use command module load tophat. This will load the default version.

Further Reading

Fields of Science: