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  • dp05yk
    replied
    During the index phase, all N's in your reference (index) sequence are converted to a random base.

    Leave a comment:


  • Protaeus
    started a topic BWA with reference containing N's

    BWA with reference containing N's

    Should I expect anything out of the ordinary by using a reference containing N's when aligning a paired end sample with BWA? It runs fine, which I would expect, but I wasn't sure if there were issues that I should look for in the output.

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