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:
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 without restriction to all OSC users.
Publisher/Vendor/Repository and License Type
http://ccb.jhu.edu/software/tophat, Open source
Usage on Owens
To configure your enviorment for use of TopHat, use command
module load tophat. This will load the default version.