Tophat
Revision as of 19:52, 16 May 2013 by Moskalenko (talk | contribs)
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.
Required Modules
Serial
- tophat
System Variables
- HPC_{{#uppercase: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.