Download Meander application and source code here.
Detailed descriptions about the file formats and their syntax can be found in the Manual.
A Powerpoint presentation is available here.
TO RUN the application you will need a Java version greater than 1.6
You should first go to the folder where the jar file is located.
To pre-process the data and create a .meander file containing all of the information at different zoom levels type:
$> java –Xmx1G -jar Meander.jar -chr chromosome -org organism -pre input_file
input_file: please provide the full path of the file containing the RD information
chromosome can be a string (1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17.....,X,Y)
organism : rat, mouse, human, arabidopsis, zebra, chimp, drosophila
example:
java -Xmx1G -jar "./Meander/Meander.jar" -org human -chr 20 -pre PD4198b_B8FF4C_B8FB3A_A6GD7A_A6GE4F_Chr20_normalized.txt
While pre-processing, in command line you will see the messages :
Creating files for zoom level...1
Creating files for zoom level...2
Creating files for zoom level...3
Creating files for zoom level...4
Creating files for zoom level...5
Often one one wants to save time and only see the initial picture and avoid analyzing the data in deeper zoom levels. Therefore you can anytime stop the process (ctrl+C) once the next zoom level message appears. For example if you want to analyze the data in two zoom levels you should stop the iteration once the the message Creating files for zoom level...3 appears.
To load a .meander file directly with all of the coverage information at different zoom levels try:
$> java –Xmx1g -jar Meander.jar -rd input_file
It should be a (.meander file)
To load a .txt file containing a chromosome information for a specific zoom level try:
$> java –Xmx1g -jar Meander.jar -rd input_file
It should be a (.txt file)
Alternatively after having pre-processed the data you can always load the files manually through the GUI .