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Changing Tophat 5' and 3' splice-signal criteria

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  • Changing Tophat 5' and 3' splice-signal criteria

    Hi,
    I need to change Tophat's splice signals criteria for junction calling (i.e. add more signals to those that tophat considers: ["GT-AG", "GC-AG" and "AT-AC"]).
    Does anyone know in which file this filter is implemented?

    Thank you,
    Gilad

  • #2
    Hey GiladZil,

    did you every figure this out?

    I'm wondering if there is any way to relax these constraints or override them..

    Cheers!!
    Carmen

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