tophat

Overview

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.

Versions 2.0.7 and 2.0.9 binaries are available.

Restrictions on use

All users may access and use Bowtie. The software is open source. Users should consult the following file for further information: $TOPHAT_HOME/$TOPHAT_VER/COPYING

Set up procedure

To use the software you must load the modulefile:

module load apps/binapps/tophat/2.0.7

module load apps/binapps/tophat/2.0.9

Running the application

Coming soon…

Further info

• The Tophat website has a manual, FAQ and index and annotations downloads.
• Related applications available on the CSF: Bowtie and Cufflinks