Difference between revisions of "Cufflinks"
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Moskalenko (talk | contribs) m (Text replace - "Usage policy" to "Usage Policy") |
Moskalenko (talk | contribs) m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#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 | ||
Revision as of 16:55, 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.
Available Versions
- 1.0.3 - Legacy version.
- 1.1.0 - This is the version used by Galaxy. Beware the file format change from 1.0.3.
- 1.3.0
- 2.0.0
- 2.0.2 - default.
Required Modules
Serial
- cufflinks
- HPC_CUFFLINKS_BIN - executable directory
- HPC_CUFFLINKS_DOC - readme directory