Difference between revisions of "Tophat"

Latest revision as of 16:39, 22 August 2022

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.

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:NGS]][[Category:Biology]][[Category:Sequencing]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|tophat}}
 |{{#vardefine:url|http://tophat.cbcb.umd.edu/index.html}}
-<!--Compiler and MPI settings - OPTIONAL -->
+|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
-|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
-<!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
-|{{#vardefine:exe|}} <!--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 38: / Line 23: @@
 <!--HPC pre-built Bowtie Indexes are located in ''/scratch/hpc/bio/bowtie''. They should be available for bowtie use automatically. If you have additional indexes that could be of use to UF Biological Community please contact us and we'll add them to the reference file space.-->
+<!--Modules-->
-==Available Versions==
+==Environment Modules==
-* 1.3.0.
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* 1.3.3 beta.
+==System Variables==
-* 1.4.1 (default).
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-<!-- -->
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 * HPC_TOPHAT_BIN - executable directory
 * 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. To be safe, add another ppn in any case.
+|}}
 {{#if: {{#var: conf}}|==Configuration==
 See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}