Immunoglobulin Galaxy

From EMC Bioinformatics
Jump to: navigation, search
IGGalaxy VM ready to be used.
The running virtual machine.

ImmunoGlobulin Galaxy provides a set of tools for easy detection and quantitation of immunoglobulin heavy chain alternative transcripts. This service is available for downloads as a virtual machine as a Galaxy service.




Open up the virtual machine.
Figure 1
Type the address into your browser.
Figure 2

How to use Immunoglobulin Galaxy

  • Unpack the above archive with your favorite unpacking tool (7zip, Winrar ,‎ Winzip).
  • Install VMWare player (https://my.vmware.com/web/vmware/free#desktop_end_user_computing/vmware_player/6_0)
  • Click on "Open a Virtual Machine" and browse to the location where you unpacked the archive (Figure 2)
  • Double click the newly added virtual machine, and it will start booting up.
  • After waiting for a few seconds, you will be presented with a welcome screen, type the address displayed in the virtual machine into your web-browser, Galaxy will be ready to use (Figure 2).
  • Registering an account will allow you to have multiple histories, you can register a new account under the "User" option at the top of the Galaxy screen. (Email address doesn't have to be real).
  • You can also login with the username "admin@galaxy.com" and the password "galaxy", this will give you access to an administration account.
  • The administrator account has a history that runs through the S22 sample.
An overview of galaxy.
Figure 3
The upload file tool view.
Figure 4

How to use Galaxy

After successfully getting Galaxy up and running, you will be presented with the Galaxy home screen (Figure 3). On the left (green) there are the tools available and on the right the current history (red). The center (yellow) will be used to show the input options for the tools and the output of the tools.

The first thing we need to do is upload some data to work with, go to the tools section, click on "Get Data" and then on "Upload File". You will be presented with the "Upload File" tool's options in the center view (Figure 4).

Browse to the fasta file you want to upload (for example the Stanford S22 sample Stanford S22 sample) and click on execute. The file will appear blue in your history while its uploading, it's best to wait until it turns yellow or green before doing anything else with Galaxy. If you are uploading an IMGT ZIP file instead, use the "Upload Zip File" tool instead.

igBLAST

The igblast tool view.
Figure 5
The igblastparser tool view.
Figure 6
  • Once you have uploaded your fasta file, it will be available for selection inside the igBLASTn tool (Figure 5)
  • After the igBLASTn tool has finished, the required data can be extracted and parsed with igBLASTparser into the proprietary format required by the rest of the tools (Figure 6).
The imgt loader tool view.
Figure 7

IMGT

  • Once you have uploaded the IMGT zip file, it will be available for selection inside the IMGT Loader tool (Figure 7)
The experimental design tool view.
Figure 8
The report tool view.
Figure 9

Experimental Design and Report

  • Merge several files together with the "Experimental Design" tool (Figure 8).
  • Use the output of the "Experimental Design" tool as input for the "Report" tool (Figure 9).
  • The result will be available by clicking on the eye icon in the final history item.