Difference between revisions of "Cufflinks"

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m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]]
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{|<!--Main settings - REQUIRED-->
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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/"
 
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MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
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{|
 
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|{{#vardefine:app|cufflinks}}
 
|{{#vardefine:app|cufflinks}}
 
|{{#vardefine:url|http://cufflinks.cbcb.umd.edu/}}
 
|{{#vardefine:url|http://cufflinks.cbcb.umd.edu/}}
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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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Cufflinks is a part of the [[Tuxedo]] suite.
 
Cufflinks is a part of the [[Tuxedo]] suite.
 
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<!--Modules-->
==Available Versions==
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==Environment Modules==
* 1.0.3 - Legacy version.
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* 1.1.0 - This is the version used by Galaxy. Beware the file format change from 1.0.3.
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==System Variables==
* 1.3.0
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* 2.0.0
 
* 2.0.2 - default.
 
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{{#if: {{#var: mod}}|==Execution Environment and Modules==
 
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
 
* HPC_CUFFLINKS_BIN - executable directory
 
* HPC_CUFFLINKS_BIN - executable directory
 
* HPC_CUFFLINKS_DOC - readme directory
 
* HPC_CUFFLINKS_DOC - readme directory
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{{#if: {{#var: policy}}|==Usage Policy==
 
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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 14:17, 15 August 2022

Description

cufflinks website  

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

Cufflinks is a part of the Tuxedo suite.

Environment Modules

Run module spider cufflinks to find out what environment modules are available for this application.

System Variables

  • HPC_CUFFLINKS_DIR - installation directory
  • HPC_CUFFLINKS_BIN - executable directory
  • HPC_CUFFLINKS_DOC - readme directory