I have been trying to find the copy number variation for the knocked in mCherry gene in U2OS cells. I am using the Thermofisher TaqMan Copy Number Assay kit with the custom probe for the mCherry and RNaseP as a reference gene. After obtaining the Ct values and uploading them to the ThermoFisher CopyCaller software I get the copy number prediction, however, the confidence number is very low for some samples. I firstly thought that it depends on the variation of Ct between the replicates which would be a technical problem, however I have a sample with a very low variation which also shows a really low confidence for the predicted copy number.
Has anyone used this software and run into the same issue?
Kind regards,
Anastasiia
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