This is an initial distribution of TopHat.  Only OS X and Linux are supported at the moment. The manual and more detailed installation instructions are hosted at http://tophat.sourceforge.net/ 

To use TopHat, type 'configure' and then 'make' from within this directory.  Add this directory to your path.

TopHat depends on Bowtie and Maq.  Please install both and add their binaries to your path.

You will also need GNU awk and Python 2.5 or greater, both of which are installed by default in most Linux and OS X systems.

You will need a Bowtie index installed, along with a Maq .bfa file the reference to use the pipeline.  Please see the script 'tophat' in this directory for more information.  The Bowtie index consists of two files such as m_musculus.1.ebwt and m_musculus.2.ebwt.  The Maq .bfa file must have the same prefix as the Bowtie files.  E.g. m_musculus.bfa

To run TopHat, type for example 'tophat /path/to/bowtie/index/m_musculus reads.fq
