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Old 08-11-2015, 10:49 AM   #1
MicroSal
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Location: Ohio

Join Date: Aug 2015
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Default Help with Fragmentation analysis using GeneMapper software

Hello,

I've been running a fragmentation analysis for microsatellites for a number of months now. All of a sudden my GeneMapper runs using an ABI 3730 and ABI 3130xl have been giving me an increasing number of failed samples. I am using Peak Scanner 2 software to call my peaks manually. Samples that ran well show peaks for both 600 Liz standard and peaks for each of my primers. Failed samples produce a blank (No standard peaks or sample peaks).

The primers amplified fine after PCR and I have seen amplication on gels before submitting to either machine. I pooled my primers together into a psuedo-multiplex with 3 primers per plate.

Even samples that ran fine a month ago failed to run correctly when submitted recently with new HiDi and 600 Liz standard. Other researchers using the machines to run Big Dye samples have worked fine.

Does anyone have any idea why I may be getting blank runs on both a 3130xl and 3730 using GeneMapper?
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Old 10-13-2015, 01:55 PM   #2
Angelmass
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Location: California

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Is it possible that your capillaries might be blocked? You say that the Big Dye samples have run fine, but were they in the same wells?

Also, have you looked at the array viewer for the wells of your problem samples?

edit: I just realized you posted this 3 months ago. Hopefully you figured out your problem!
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