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pregap4 und phrap quality values

deKesi
2006-08-30
2013-04-18
  • deKesi
    deKesi
    2006-08-30

    Hello,

    the current version of phred (020425) writes phred base quality values in .scf files.
    This information is stored in the following part:

    uint_1 prob_A;
    uint_1 prob_C;
    uint_1 prob_G;
    uint_1 prob_T;

    If the called base is 'A' then the quality value is stored in 'prob_A' and so on.

    Now I would like to know if the current version of the io_lib is capable of extracting these values from . scf - files an write it to the .exp - files.

    Due the lack of not having the current phred version, I'm not able to test this myself.

    I would appreciate any help or comments on this.

    Kind regards,

    squig

     
    • deKesi
      deKesi
      2006-09-15

      Hello,

      finally it seems I found a answer to my question.
      On http://staden.sourceforge.net/phrap.html can be found following information:

      "The 1998.0 and later releases of Gap4 includes changes that make it easy to combine Phil Green's Phrap assembly engine with the Gap4 editing and finishing tools."
      ...
      "This is only relevant for Phrap version 0.98* and newer."
      ...
      "The "Phred" module in Pregap4 will recall the trace bases and will store the new base calls and confidence values in the SCF file."

      I will run a test in the next days just to confirm this information for myself.

      Kind regards,

      deKesi