Difference between revisions of "Tophat"

Revision as of 19:52, 16 May 2013

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

modules documentation

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.

@@ Line 5: / Line 5: @@
 |{{#vardefine:app|tophat}}
 |{{#vardefine:url|http://tophat.cbcb.umd.edu/index.html}}
-|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
+|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
@@ Line 33: / Line 33: @@
 * HPC_TOPHAT_DOC - documents directory
 {{#if: {{#var: exe}}|==How To Run==
-WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
+'''Note:''' If your data is compressed your job script should add another ppn to accommodate the external gzip process tophat will run.
+|}}
 {{#if: {{#var: conf}}|==Configuration==
 See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}