== TopHat RNASeq alignment software ==
The software and instructions can be found on: http://tophat.cbcb.umd.edu

=== Mykopat Grid specifics ===
There is a good protocol describing the basic usage published, and links to it are available from the homepage. However, the protocol lacks information about how to create the genome index. This should be done with the `bowtie2-build`command

{{{
$ bowtie2-build my_genome.fas my_genome
}}}
where my_genome is what will be given to tophat (prepended with the path to where it resides). For typical fungal genomes, index build takes a few minutes for fungal genomes. For larger genomes it can take up to a few hours, and then it has to be submitted as a job to GridEngine.

Tophat runs usually requires a 1-2 GB ram, takes several hours to run and thus has to be submitted as GridEngine jobs.