There's this PCR product on all my samples of one species (first image) that amplified and is detectable but does not look the way the other alleles look so I don't know if I should be including it as an allele for the analyses or is this how a null allele looks? And if that's the case, should I include it with my dataset? The second image shows the PCR products for the second species I'm analyzing. You can see that the same product amplifies but looks almost exactly as the other alleles.
you should be considered all of those microsatellite in your analysis which give very good sharp single distinguishable peaks. Those micro satellites shoud be excluded which giving either upper or lower tails in the PCR.
Dear Ujjal,
I suggest you include all those alleles that conspicuously exceed the cutoff value and discard those that do not "stutter". The discrepancies that you find in your amplifications can be analyzed in depth to get to consider them null alleles, based on the complexity of their amplification and detection by PCR, an alternative could be a deep sequencing. I leave you a review about null alleles and how to detect them.
Best regards
https://www.nature.com/articles/6800545
I agree with the others and I would also exclude the first microsatellite because if it behaves in this manner with all your samples, you won't have any information anyway. You need a good polymorphic marker easy to detect.
Hello I think you have a confusion a null allele is an allele that can not be amplified, for example if you have an individual that is heterozygous for a certain microsatellite locus, but only one allele was amplified, in your electropherogram you would have only one peak, it was believed to be a homozygous but it is not. Then the null alleles you can not see.
The null alleles cause an overestimation of homozygotes and exist programs to verify the presence of null alleles, such as MICROCHECKER software and then analysis to know if the presence of null alleles significantly modify your results FREENA. If you see peaks in your electropherograms that do not have the allele form of that microsatellite, you may stutter and do not consider it. Guiate by the way
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