Cufflinks is a useful program for managing and analyzing RNA-seq data. Cufflinks, along with the included cuffcompare, cuffdiff, cuffmerge, cuffnorm, cuffquant, gffread, and gtf_to_sam programs, can all be downloaded in a pre-compiled .tar file from from their download site. Just be sure to download the most recent version of the Linux distribution if you want to put it on a UNIX machine. To install cufflinks, simply follow these steps.
(1) Untar the cufflinks-0.0.0.Linux_x86_64.tar.gz in the desired directory you want to place cufflinks
(2) Add the following line to you .bashrc file and then type source .bashrc.
The above example uses cufflinks-0.0.0 as an example version. This needs to be changed in the above code to match the current version.
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