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  • jcreecy
    Junior Member
    • Apr 2012
    • 1

    #1

    RNA seq with Illumina

    I have looked into a number of protocols for directional RNA seq on Illumina, and I would like to use a ligation based method. Before I started I want to get additional opinions. Would it be possible to conserve directionality be ligating a 6-8nt barcode to both the 3' and 5' end of the RNA prior to following the standard protocol for ligating the Illumina adapters? If so, what complication should I be looking out for?
  • mikaelk
    Member
    • Jun 2012
    • 11

    #2
    Hi,

    As far as I know having barcodes ligated directly to the fragmented RNA is a bad idea and I would not recommend that.
    The ligase is not having the same efficiency to ligate with different set of sequences (here your barcodes).
    But in theory, it should be possible.

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