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  • [ddRAD] on removal of duplicate reads

    Hi All,

    Is it advisable to remove duplicate reads from double digest RAD (ddRAD) data generated on Illumina Hiseq platform ?

    Regards,
    Krishna

  • #2
    ddRAD libraries has two types of duplicates:

    1- PCR duplicates
    2- duplicates rising from input genome equivalent used for dig-lig

    As most of ddRAD protocols does not use UMIs, it is not possible to distinguish those.

    Throughout analysis a minimum coverage is used to form stacks of RAD-tags, catalog and estimate zygosity for the called genotypes so duplicates should not be removed.

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