TopHat
Description
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.
License
Boost Software License, Version 1.0
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of tophat and load default version of tophat as
module avail tophat/ # list available modules module load tophat # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail tophat
and choose explicit version you want to use.
Documentation
https://ccb.jhu.edu/software/tophat/manual.shtml