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Old 10-19-2017, 12:25 AM   #4
Genetic Librarian
Location: Europe

Join Date: May 2017
Posts: 31

My wild guess would be on low ligation efficacy, giving the final PCR no target to amplify.
If that is true, you can check that by quantifying your library by Qubit and by qPCR (e.g. Kapa library quant for Illumina). Normally, with a ligation efficacy of ~50%, your Qubit value would be twice as high as your qPCR value. If your library does not contain adapters (or very little), qPCR value should be waaaaay lower.
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