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  • primer design

    Are there any recommendations for bioinformatics of multiplex primers? Maybe GC content, secondary structure, etc... I seem to be having an issue with a primer design that was not an issue for our first panel. For example, using NA12878 with the first primer design (395 amplicons):

    On-Target Reads- 95%, End to End - 85%

    NA12878 with the second primer design (923 amplicons):

    On-Target Reads- 60%, End to End - 80%

    Thank you.

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