Can I use a custom microsatellite ladder?

Custom ladders can be added from plugin version 1.2 onwards.  Ladders are stored in a text file which can be manually edited to add new ladders. 

The ladders.txt file contains a tab-separated list of ladders where the first field is the name of the ladder and the rest are the ladder fragment peak sizes in bp. If you edit this file then Geneious must be restarted for changes to take effect.

 

Locating and editing the ladders.txt

First, ensure you have installed the Microsatellites plugin is installed via menu Tools -> Plugins.

The ladders.txt file can be found in the microsatellite plugin installation directory:

If you do not have admin privileges it will be installed in your home directory in

Geneious X.Y data/Plugins

Within this directory you will find the microsatellites plugin folder named:

com.biomatters.plugins.microsatellite.MicrosatellitePlugin

Within this folder you will find a series of subfolders:

com\biomatters\plugins\microsatellite\data

and within data directory you will find the ladders.txt file. 

 

If the plugin folder cannot be found in your data folder, try the following locations:

On a mac:

/Library/Application Support/Geneious/plugins/...

On Windows:

C:/Users/username/AppData/Local/Geneious/plugins/...

Note: The Appdata folder is a hidden folder.  To find it you will have to go to Folder Options in the Windows Control Panel, and in the View panel and check the option to "show hidden files, folders and drives".

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