tophat

Module Name

tophat

Last Updated On

08/29/2023

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

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

Default

2.0.13

Other Modules

1.4.1, 2.0.10, 2.0.11, 2.0.12, 2.0.13, 2.1.1

Default

2.0.13

Other Modules

1.4.1, 2.0.10, 2.0.11, 2.0.12, 2.0.13, 2.1.1

Default

2.0.13

Other Modules

1.4.1, 2.0.10, 2.0.11, 2.0.12, 2.0.13, 2.1.1