FAQ: Can I assess PCR-free library quality on a BioAnalyzer and/or TapeStation?

Precautions should be taken when using Bioanalyzer and TapeStation to assess quality of PCR-free libraries. Bioanalyzer and TapeStation can be informative at revealing whether PCR-free libraries are contaminated with leftover adaptors or adaptor dimers. However, size estimation and library quantitation are not accurate on Bioanalyzer and TapeStation. The long, single stranded region of the PCR-free adaptors interfere with migration of PCR-free libraries, making them appear to be much larger. In addition, Bioanalzyer and TapeStation cannot differentiate between input DNA fragments and DNA fragments with one or two adaptors ligated, which makes them unsuitable for quantitation. We recommend qPCR for library quantitation of PCR-free libraries.