Install Cufflinks on a UNIX Account

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.

Installing Tabix on UNIX

Tabix is an incredibly useful tool that indexes large .vcf files and makes it very efficient to find a particular genomic region in the file.  It is particularly useful for downloading small portions of files from publicly available ftp data repositories.  Here is a brief tutorial on how to install Tabix on a UNIX operating system.

(1) Go here to download the newest release.
(2) Extract the file:

(3) Compile the program by typing make on the UNIX command line.
(4) Export the path by adding the following line to your .bashrc file, saving your .bashrc file, and typing source on the UNIX command line.  Note: path_to_tabix is the directory where tabix is installed.