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