Difference between revisions of "Cufflinks"
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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 is a part of the [[Tuxedo]] suite. | Cufflinks is a part of the [[Tuxedo]] suite. | ||
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==Required Modules== | ==Required Modules== | ||
[[Modules|modules documentation]] | [[Modules|modules documentation]] | ||
===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
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* HPC_CUFFLINKS_BIN - executable directory | * HPC_CUFFLINKS_BIN - executable directory | ||
* HPC_CUFFLINKS_DOC - readme directory | * HPC_CUFFLINKS_DOC - readme directory | ||
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WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 18:08, 10 August 2012
Description
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.
Required Modules
Serial
- cufflinks
System Variables
- HPC_{{#uppercase:cufflinks}}_DIR - installation directory
- HPC_CUFFLINKS_BIN - executable directory
- HPC_CUFFLINKS_DOC - readme directory