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.

TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology.

Programs location

/usr/local/tophat/bin

Version

1.0.10; July 30, 2009

How To Use

Please add bowtie and tophat binaries to your path:

For tcsh users:

For bash users:

Example files below can be copied from /usr/local/tophat/example/test_data.tar.gz

Documentation

http://tophat.cbcb.umd.edu/tutorial.html