Tophat - A Spliced Read Mapper for RNA-Seq

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] [reads1[,reads2,...,readsN]


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

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