What dyes does Geneious Prime recognise?

Geneious will pick up whatever dye(s) are listed in the microsatellite trace file. The last dye is assumed to be the ladder. 

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    Samantha Robison

    I recently had a fragment analysis run on a 3730xl capillary electrophoresis machine calibrated for the DS-33 dye set (6FAM, VIC, NED, PET, LIZ). I used ROX 500, which is detected under the PET channel. I'm having trouble with Geneious recognizing my ladder -- PET isn't detected as the last dye on the trace (it is detecting LIZ as the last one). Is there a way I can remove LIZ or get around this so that my ladder can be recognized?

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    Laura Torrado Blanco

    Hello Samantha, I find myself in the exact same situation. Have you found a solution for this?

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    Hilary Miller

    Hi Samantha and Laura, unfortunately there is no easy way around this. The Geneious microsatellite plugin is designed to detect your ladder in the last dye of your file. Normally you either have 5 dyes and the ladder is in the 5th dye (LIZ), or you have a 4 dye setup with 4 dyes on the trace and the ladder (usually a ROX ladder) in the 4th dye. However in your traces, there are 5 dyes set up but the ladder is in the 4th dye (and the 5th dye is empty), so Geneious won't recognise it.

    If you are able to re-run your samples and use a 4 dye set configuration that might be the easier way to fix it. In Geneious the only workaround is to select all of the peaks in the PET dye by clicking on them (hold down command while you click to select multiple peaks), and then going to Add Peak-> To LIZ. Once the peaks are in LIZ the ladder should be recognised.

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    Laura Torrado Blanco

    Hi Hilary, thank you for your quick reply. I tried a few things and I ended up with the same solution you reccomend: manually adding the peaks to the LIZ channel seems to be working fine. I will try to fix the dye setup on the next runs to avoid this issue as you suggest.
    Again, thank you so much for your help.