Difference between revisions of "Documentation"

From GenPlay, Einstein Genome Analyzer

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== General Options ==
 
== General Options ==
 
The following screen let you set the general options:
 
The following screen let you set the general options:
[[image:general_options.png|right|thumb|100px|General Options]]
+
[[image:general_options.png|center|thumb|100px|General Options]]
 
The Default Directory lets you specify where the files containing GenPlay tracks will be stored in your file system.
 
The Default Directory lets you specify where the files containing GenPlay tracks will be stored in your file system.
 
The Log File is a text file that contains a time-stamped history of the files extracted and loaded on GenPlay.  
 
The Log File is a text file that contains a time-stamped history of the files extracted and loaded on GenPlay.  

Revision as of 16:37, 22 November 2010


Starting GenPlay

To start GenPlay, click the button corresponding to the amount of memory that you wish to allocate to the Java virtual machine. This amount of memory determines how many tracks you will be able to load at the same time. The programming philosophy behind GenPlay is to provide extremely fast performances once the data are loaded. To achieve that goal the entire genome can be loaded in memory for multiple tracks at the same time. This results in really nice performances but the cost is a requirement for a lot of memory. The amount of memory needed per track depends on the genome, the track type, the window size, the data precision etc. You should generally choose as much memory as you can afford on your system (generally about 70% of the total RAM memory that exists on your system). For mammalian genomes we recommend allocating at least 4 GB of RAM although you should be able to load a couple of genome-wide tracks with 1GB or 1.5GB of RAM. Selecting analysis of only one chromosome at a time will drastically reduce the memory requirement and should allow you to load many tracks at very high resolutions. Tracks loaded in GenPlay can also be compressed (see below.) The amount of RAM memory available to GenPlay is displayed in the lower right corner of the screen

Changing the configuration of GenPlay

On GenPlay’s main screen click on the top left button (shown by a little hammer and spanner) to pop up the following screen

Option Menu

General Options

The following screen let you set the general options:

File:General options.png
General Options

The Default Directory lets you specify where the files containing GenPlay tracks will be stored in your file system. The Log File is a text file that contains a time-stamped history of the files extracted and loaded on GenPlay.

Choosing a genome

Once GenPlay is started a configuration file describing the genome that you want to analyze (the default is human hg18). Configurations are simple text file that specify the name and length of the chromosome of the current genome. Configuration files for human and mouse recent assembly can be downloaded from the GenPlay library accessible from the GenPlay.net web page (please see below). Configuration files for any genome can easily be created in any word processor using the provided examples as a model.