Difference between revisions of "Tophat"

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(Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:Bioinformatics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in temp...")
 
 
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[[Category:Software]][[Category:Bioinformatics]]
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[[Category:Software]][[Category:NGS]][[Category:Biology]][[Category:Sequencing]]
<!-- ########  Template Configuration ######## -->
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{|<!--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:app|tophat}}
 
|{{#vardefine:url|http://tophat.cbcb.umd.edu/index.html}}
 
|{{#vardefine:url|http://tophat.cbcb.umd.edu/index.html}}
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
 
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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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 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.
  
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<!--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.-->
 
<!--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.-->
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{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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==Environment Modules==
==Available Versions==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* 1.3.0 - default.
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==System Variables==
* 1.3.3 beta - will become default when released as a final version.
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
<!-- -->
 
{{#if: {{#var: mod}}|==Running the application using modules==
 
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
 
* HPC_TOPHAT_BIN - executable directory
 
* HPC_TOPHAT_BIN - executable directory
 
* HPC_TOPHAT_DOC - documents directory
 
* HPC_TOPHAT_DOC - documents directory
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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'''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.
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|}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 16:39, 22 August 2022

Description

tophat website  

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.