In Galaxy TopHat has been replaced with HiSat or HiSat2. When following Galaxy tutorials replace TopHat commands with HiSat or HiSat2.
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 run this software in a Linux environment run the commands:
module load tophat tophat [options]
Current default version loaded by "module load tophat": 1.4.1. New version loaded by "module load tophat" after upgrade January 14, 2013: 2.0.5. To continue loading the old version use:
module load tophat/1.4.1
Once you have set up your environment, you can run the program directly from the command line. eg
tophat [options] [reads1[,reads2,...,readsN] Compatibility issue: The new version of Tophat uses Bowtie 2.X instead of Bowtie 0.X, and therefore uses Bowtie 2.X genome indexes. Significant changes (improvements) have been made to Tophat command-line options, and to how Tophat performs alignments. Reference indexes: The genome indexes could be found at /panfs/roc/rissdb/genomes