JETTA: GUI Tutorial



Overview

The JETTA GUI implements a graphical user interface on top of the JETTA package. Co-working with the JETTA command line applications, R and cisGenomeBrowser, it provides an easy way of analysis and visualization. Many thanks to Shangping Feng, who initially implemented this program.
This tutorial is based on the Glue Grant arrays of liver and muscle. We will go through the expression and alternative splicing calculations, clustering analysis of expression matrix, alternative splicing detection, and visualization of alternative splicing signals and raw-level signals.

For the detail usage of GUI for RNA-Seq data, please see The Use of JETTA for RNA-Seq.


Preparation

Download the liver/muscle arrays and the corresponding library and annotations. For the full functions, CLF, PGF, MPS, Probe Position File, Alternative Splicing Structure, Probe Position File and dChip Annotation are needed as well as genome annotation files for cisGenomeBrowser. An example of the genome annotation files can be found here, and other libraries can be found on the top page. The JETTA GUI is based on JAVA. MAC/Linux systems support JRE(Java Runtime Envrionment) by defaults, but Windows do not. Before using the JETTA GUI, Windows users need to install JRE unless they already have. R should be also installed.


Starting a new project

By clicking [Analysis]->[New], users can start a new project. On the [Project] panel, users can set up a project name, data directory and analysis type. For this tutorial, please set 'Analysis' field as ASA. Then, set libraries on the [Library] panel, and leave other parameters as defaults. For details of parameters, please refer the description on the param.conf. After setting all parameters, press [Done] on the [Project] panel, and save the project.



Running the JETTA

After starting a new project or opening a saved project, users can start expression/alternative splicing calculations by clicking [Analysis]->[Run JETTA]. This step takes for a while. When "Probe Position File" on the [Library] panel is specified, the JETTA generate BAR files, which takes a long time. After this step is completed, users can find 'log.txt', 'expr.tc.out.txt', 'asa.out.txt' and several bar files under 'out.jetta' directory. These are common outputs of the JETTA.



Setting the RScript path

In Windows systems, user need to set the Rscript path. It is usually under C:\Program Files\R\R-x.x.x\bin. R automatically sets its path for MAC/Linux systems, but users may need to set it unless it is included in user path. User can set the RScript path by clicking [Tools]->[Specify RScript].


Clustering analysis

User can performe clustering analysis for expression matrix by clicking [Tools]->[Clustering]. User can specify input expression matrix, and criteria for gene selection. Selecting too many genes might cause memory problems.



Detecting alternatively spliced exon candidates

[Tools]->[ASA Filtering] opens a window to detect alternatively spliced exon candidates. For the details of each criteria, please refer the help file of jetta.asa.filtering function of the JETTA R-package. ASA file should be the output of the ASA/MADS analysis. dChip annotation can be set optionally. Please use "xxx.gene info.xls". Any annotation file can be used if tap-limitted, the first column is gene id, and the last column is the symbol.



Showing alternatively spliced exon candidates

[Tools]->[Showing ASA Candidates] shows the detected candidates from the previous step. Please check "Show exon only" and "Show selected only" to prevent memory problems. By clicking the gene id(TC column), user can see the alternative splicing signals of exon and junctions with gene structure.



cisGenomeBrowser (Windows only)

The JETTA GUI can generate BAR files and call the external cisGenomeBrowser. Since cisGenomeBrowser supports Windows systems only, this function is limited to other platforms.
By clicking [Tools]->[cisGenomeBrowser], user can set genome annotations and CEL files to be displayed. The genome annotation files should be reflat format or other formats that cisGenomeBrowser allows. Multiple annotations can be added by [Add one more], and the existing ones can be removed by [Delete]. Users need to specify the cisGenomeBrowser directory, where 'display_server.exe' locates.



By clicking [Done], the Internet Explorer pops up and open the cisGenomeBrowser page. For more functions of the browser, refer to cisGenomeBrowser webpage.






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