Geneious Prime doesn’t recognise my ladder - how do I fix it?

This may happen if the trim is not set correctly, if the ladder peaks are too low, or if there are extra or missing peaks. First check the trim is set correctly.  You may then need to manually call the peaks as follows:

1. Disable viewing all trace dyes except your ladder.

2. Enable the 'Show Traces', 'Show Peak Calls' and 'Show Peak Labels' options, and increase the Y scaling to its maximum extent so you can clearly see the peaks, and increase the X scaling so the peaks are wider.  

3. Add missing peak calls by clicking the point where the peak call is and then click the 'Add Peak' button in the toolbar.  Remove extra peaks by selecting the peak and clicking the "Remove Peak" button in the toolbar. Check for stutter peaks and remove the shorter of the pair. After you've edited several peaks, Geneious will recognise what ladder it is. You'll see the name of the ladder under the dye name in the panel to the right.

If you are using a custom or unusual microsatellite ladder, you may need to add the ladder to Geneious before it can be called.  See this post for instructions.  

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    I am having this problem.  However, when I tried to do what you said, I was unable to find the "Add Peak" button on any of my toolbars.  Can you direct me to where this is?  I am using version 7.1.5.   Also, I am having this issue with virtually all of my samples, any idea why and is there an easy way to correct this for a batch of samples, rather than one at a time? Thanks.

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    Hilary Miller

    The Add Peak button is directly above the Trace viewer, as shown below.  You need to select the peak you want to add before the button becomes active.  



    It is possible to add peaks to multiple traces at once.  Just select all the traces you want to view while holding down the cntrl/command key, then select all the peaks in each trace that you want to add and click the Add Peak button to add them all at once.  

    If you are still having difficulties, please submit a support request with one of your files attached and we would be happy to take a closer look. 

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    I am having the same problem. When I choose the peaks, there is no add peak button.

    It looks like Geneious does find the ladder peaks but cannot fit them so when I choose the peaks I can delete them

    How can I assign sizes to the ladder peaks when Geneious cannot fir the ladder?

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    Hilary Miller

    If there is no Add Peak button, then it means that peak is already added.   The Geneious ladder calling algorithm uses the distances between peaks to call the ladder, so it is not possible to set the peak sizes yourself.  In some cases extra peaks are called that will confuse the algorithm, so these will need to be removed.  It helps to have some idea of what your ladder should look like when determining whether to add or remove peaks.  I'd be happy to take a closer look at why your ladder isn't being called - just contact us via the Support button in Geneious with an example file where you can't fit the ladder.



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    Olga Kozhar

    Could you please advice if I can fit ladder to all of my files automatically after I do it manually to the first one? I have quite large sample size and see that have to fit ladder (the same one) to each of the file manually which takes a lot of time. Thank  you

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    Moreland Gibbs

    You will have to manually fit the ladder to all traces where the ladder has not been recognised. 

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    Is there any way to adjust the height of the peaks that it recognizes? For the ladder it is calling the very small shadow band after before each peak, really time consuming to have to manually remove every shadow band.

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    Hilary Miller

    You can adjust the peak height call threshold by clicking Predict Peaks->For LIZ and then checking "change peak height call threshold" and increasing the number.