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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