Cufflinks

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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.

Availability

Version 2.0.2 and 2.2.1. Available modules:

cufflinks-2.2.1
cufflinks-2.0.2

Use

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:

-p $TORQUE_RESC_PROC

Documentation

http://cufflinks.cbcb.umd.edu/

Licence

Boost Software License, Version 1.0

Program manager

meta@cesnet.cz

Homepage

http://cufflinks.cbcb.umd.edu/