cufflinks

About

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.

Versions and Availability

Module Names for cufflinks on smic
Machine Version Module Name
smic 2.1.1 cufflinks/2.1.1
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Usage

Cufflinks comes with several tools, such as:
    cufflink
    cuffcompare
    cuffdiff
    cuffmerge
    gffread

The details of options and parameters required for using each tools can 
be displayed typing "toolname --help".
    

Resources

Last modified: June 21 2015 10:55:08.