# tophat

## Summary

+ **Module Name:** tophat
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://tophat.cbcb.umd.edu/index.html](http://tophat.cbcb.umd.edu/index.html)

## Software Description

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.
## General Linux

To run this software in a Linux environment run the commands:

    module load tophat
    tophat [options] [reads1[,reads2,...,readsN]

NOTE: 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