Tophat
Jump to navigation
Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.
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.
Tophat is a part of the Tuxedo suite.
Environment Modules
Run module spider tophat to find out what environment modules are available for this application.
System Variables
- HPC_TOPHAT_DIR - installation directory
- HPC_TOPHAT_BIN - executable directory
- HPC_TOPHAT_DOC - documents directory
How To Run
Note: If your data is compressed your job script should add another ppn to accommodate the external gzip process tophat will run. To be safe, add another ppn in any case.