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  • wiggle score

    Hi,

    Does anyone know how the scores for peaks in a wiggle file are calculated? I know the vertical axis in a wig file is its score but I'd like to know a bit about what it means. (I was asked about it by a colleague and I didn't have an answer).

    Thanks!

  • #2
    In the .wig files we generate it's a count of the reads that either start at or cover that location. I suppose it could also be a normalized read count.

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    • #3
      Originally posted by captainentropy View Post
      Hi,

      Does anyone know how the scores for peaks in a wiggle file are calculated? I know the vertical axis in a wig file is its score but I'd like to know a bit about what it means. (I was asked about it by a colleague and I didn't have an answer).

      Thanks!
      It depends on the software you used. It may be the coverage or any other coverage-derived measure.

      d

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      • #4
        The wiggle score can be anything, it's a track type, not a type of measurement. For a NGS dataset, it can be raw reads (i.e. how many reads cover that bp), or normalized RPM, with or without multireads, with multiread contribution to the score estimated in some convoluted way based on unique read abundance in the neighborhood, etc, etc. It all depends on how it was generated.

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