Can I use a custom microsatellite ladder?

Custom ladders can be added from plugin version 1.2 onwards.  In this version, ladders are stored in a text file which can be manually edited to add new ladders. This file can usually be found in the microsatellite plugin installation directory (com.biomatters.plugins.microsatellite.MicrosatellitePlugin), which is usually in the Geneious X.Y data/Plugins folder in your User directory. 

Within this directory are a series of sub-directories: 
com/biomatters/plugins/microsatellite/data 

and within this directory is a ladders.txt file. 

This 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. Geneious must be restarted for changes to this file to take effect.

If you can't find the microsatellite plugin directory in your data folder try this alternative location:

On a mac: /Library/Application Support/Geneious/plugins/...

On Windows 7: C:/Program Data/Geneious/plugins/...  Program Data is a hidden folder so to find it you will have to go to ToolsFolder OptionsView and check the "show hidden files, folders and drives" option. 

Have more questions? Submit a request

Comments

  • Avatar
    Andrew Whiteley

    I am trying to add a custom ladder.  I have the microsatellite plugin v. 1.3 installed in Geneious v6.1.6 on a MacBook Air running OS X v10.7.5.  Following these instructions doesn't lead me to the ladder.txt file and I am unable to locate it by other means.  Any help would be greatly appreciated.

  • Avatar
    Hilary Miller

    Have a look in Library/Application Support/Geneious/plugins (and then the subdirectories mentioned in the post above).  Sometimes the microsatellite plugin folder ends up there.

  • Avatar
    Juan Zalapa

    Hi, 

    I had the same problem. I have Geneious installed in:


    A) Win7 and OSX 10.6 and I cannot find the plugin folder. I can find other plugins but not the microsatellite one.  

    B) In Linux the closest folder is com.biomatters.plugins.microsats.Microsats.Plugin/com/biomatters/plugins/microsats and inside I find 3 files (BatchExtract.exe, Batchextract_linux & Batchextract_mac)

    Thanks

  • Avatar
    Amy Wilson

    Juan, it sounds like you are using an early version of the Microsatellites plugin. The ladders.txt file is new in version 1.3 so if you update you should be able to find it.

  • Avatar
    Juan Zalapa

    We thought the same, but according to Geneious we are running version 1.3.0. I have uninstalled and installed it again and have the same results. 

    By the way my Geneious version is 6.1.6

  • Avatar
    Hilary Miller

    Hi Juan

    Try uninstalling your plugin, closing down Geneious, then checking that the com.biomatters.plugins.microsats.Microsats.Plugin folder has gone (delete it manually if it hasn't).  Then restart Geneious and install the latest version of the plugin from our website again and see if that fixes it.  

    On your mac did you look in that Library/Application support/Geneious folder?

  • Avatar
    Amy Wilson

    OK firstly, there is quite a bad bug in 1.3.0 which was fixed in 1.3.1 so I suggest you install that.

    When you have uninstalled the plugin, does the folder you found with the BatchExtract files in it get deleted?

  • Avatar
    Robert T. Moore

    Hi, We are trying to fit GeneScan 500 Rox, which appears to be in the ladders.txt file but still is not working. Do you have any suggestions for how to manually set the ladder information?

     

    Thanks

  • Avatar
    Hilary Miller

    Have a look at this post for instructions on how to fix your ladder so that Geneious can recognise it.  If you are still having problems after that, please contact us directly using the "Submit a Request" button on this site or the Support button in Geneious, and attach one of your traces where the ladder isn't called correctly.  We should be able to help once we can see an example of your data.

  • Avatar
    Robert T. Moore

    Hilary,

    Thanks for your response. We have tried all possible options that we could find online, including what was in that post. Any other suggestions? The ladder looks fine. We have used GS LIZ for some of our other samples and the ladder calls work fine in geneious. However, we cannot get the GS ROX ladder to work in geneious.

     

    Thanks

  • Avatar
    Hilary Miller

    HI Robert

    Could you send me one of your trace files with the ladder that doesn't work, either using the Support button in Geneious or the Submit a Request form?  It would also help to know what dyes you have used for your loci, so we can check that the dyes haven't gotten mixed up.

    Thanks.

    Hilary

  • Avatar
    luc abate

    Hi everyone,

    I'm new with Geneious (trial version) and I'm trying microsatellite (v1.4). I had some difficulties to find the ladder.txt file in the beginning, which is not located on the Program files folder but in ProgramData directory (hidden) for me (w7). Now my problem is to select my custom ladder. In fact I don't know how to change the selected ladder.

    Thanks

  • Avatar
    Hilary Miller

    Geneious will automatically call your ladder, and will choose your custom ladder if the peaks in your trace match it.  If its calling a different ladder then it may be that you have some incorrectly called peaks.  See this post for information on how to edit the ladder peaks.  If you're still having trouble with it, please submit a support request and attach a couple of example traces plus your ladder file.  

     

  • Avatar
    luc abate

    Ok, Geneious choose him self the good ladder. But I see in the ladder.txt file a row for "GeneScan 500 - no 250bp peak", and Geneious seems to choose the normal GeneScan 500 even if he popup info about the problem that can occur with the fragment 250bp. Me I use also GS500Liz but with a reducted run time on the fragment analyser which result in the loose of some ladder's fragments (450,490 and 500). It still work on geneious. But I would not like 250bp peak to be considered.

    I notice, that I try to unenable with "#" genescan 500 (in the ladder.txt file) but Geneious will not choose GS 500 with no 250 peak. It will use GS350 rox.

  • Avatar
    Hilary Miller

    You could just try removing the peak at 250 bp (click on it and choose "remove peak") and see if it switches to the correct ladder.  If not, please submit a support request and attach a copy of your file as we can't troubleshoot this further without seeing an example of your data.  

  • Avatar
    David B. Lowry

    I am testing out Geneious to see if I want to buy it, but I have run into a problem with adding a custom ladder for microsats. I am running Genenious 8.05 on a Yosemite 10.10.1 with the version 1.4 Microsatellite plugin. I cannot find the ladders.txt file. I searched for com.biomatters.plugins.microsatellite.MicrosatellitePlugin, but it does not exist. I also looked in the Library/Application Support/ directory, but there was no Geneious directory contained within it. I searched for ladders.txt and came up with no results either. So, how do I go about entering a custom ladder?

    Thanks, David

  • Avatar
    Hilary Miller

    There are actually two Library directories - one in your User directory, and the other in the root directory.  You should be looking in the one in the root directory so if you are searching from the Terminal it is

    localhost:~ hilary$ cd /Library/Application\ Support/Geneious/plugins/com.biomatters.plugins.microsatellite.MicrosatellitePlugin 

    Don't forget the initial / as that takes you back to the root (I'll amend the original post to make that clear).  

  • Avatar
    David B. Lowry

    Awesome!


    Thanks,


    David

  • Avatar
    Kim Stokmans

    Hi 

    I've done al the previous and still cant't find the ladder text file. The folder closest to the folder you are talking about is Microsats.Plugin/com/biomatters/plugins/microsats with BatchExtract.exe, Batchextract_linux & Batchextract_mac (btw I work woth windows...). I deleted this file, reinstalled the plugin, closed geneious,... But none if it works.. I looked in programData but nothing. I checked the version of the plugin (1.4) and Geneious (9.0.5)... I have no clue what to do next... I want to change the standard size to LIZ1200... Do you have any ideas what to do next?

    Thanks Kim