Difference between revisions of "Cufflinks"

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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:Biology]][[Category:NGS]][[Category:Sequencing]]
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{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
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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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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 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.  
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Cufflinks is a part of the [[Tuxedo]] suite.
==Available Versions==
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<!--Modules-->
* 1.0.3
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==Environment Modules==
* 1.1.0 - Default - (Beware the file format change)
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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==System Variables==
{{#if: {{#var: mod}}|==Running the application using modules==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{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: exe}}|==Additional Information==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
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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