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.
Version 2.0.2 and 2.2.1. Available modules:
module add cufflinks-2.2.1 cuffdiff
and other binaries, see Documentation.
For parallel computing is necessary to use the parameter
-p <number of processors>. You can take the number of reserved processors (specified by qsub command) from the torque system:
Boost Software License, Version 1.0