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.

Install SRA Toolkit on UNIX OS

SRA Toolkit is the set of programatic tools Sequence Read Archive (SRA) provides for accessing information in their .sra files.  The toolkit can be downloaded for a variety of platforms here, but in this post I will focus on installing the toolkit on a UNIX platform.

The first step is to download to the directory you want the program saved in and extract the program:

Next, you need to configure the toolkit by going into the bin directory and opening the java configuration script (make sure you have X11 forwarding enabled):

For the most part you can accept defaults when you walk through the setup, just make note of the directory you specified during configuration.  You should be all setup!  Check out other blog entries for SRA here.

How to Install Vcftools

Vcftools is a handy program to manipulate .vcf files.  This page describes how to install vcftools.  Here is a brief summary of what to do.

1) Download the most recent version of vcftools.
2) Extract vcftools using the extract command or the following line of code.


3) To build vcftools, cd into the vcftools directory and type make.
4) Add the following two lines to you .bashrc file and then type source .bashrc.


One final note: vcftools requires .vcf files be zipped by bgzip and indexed by Tabix.  To install Tabix, see these installation instructions.  Enjoy using vcftools!

How to Install Circos

A program I have wanted to learn how to use for a long time now is Circos.  The program plots visually appealing circular plots where each rung can represent a data track and data connections can be depicted with spokes.  To download, first find the most current version on their download site.  After downloading, unzip the file using tar xvfz circos-x.xx.tgz or the extract command.  If not already there, cd into the circos-x.xx directory and make sure the files are executable by typing chmod +x bin/circos.  You should then be able to cd into the bin directory and execute circos using the command ./circos.  You can also add the line export PATH=$PATH:/dirname/circos-0.63-4/bin to your .bashrc file (where dirname is the name of the directory where circos was extracted to) so that all you need to type is circos and the program is called.  Don't forget to source the .bashrc file.  Happy plotting!

Install Samtools on UNIX System

Samtools is a very useful tool for manipulating and visualizing .bam files.  Here is a quick guide on how to install Samtools.  First download the most current version from the Samtools website.  Unzip the file using either tar xvjf or the extract command.  Go into the newly created directory and compile the code by typing "make".  Your code should look something like this.

The next step is then to modify your .bashrc file so that when you type "samtools" it calls the program.  To do this open your .bashrc file and add the following line of code, where directory is equal to the directory that you have installed Samtools in.

Make sure as a final step to source the .bashrc file by entering source .bashrc into the command line.