gcphrap and gap4 bug

  • Nobody/Anonymous

    I have been playing around with running phred and phrap(gcphrap) from pregap4 and have encountered a problem (bug).
    I have configured pregap4 to run phred, initiate exp files, run phrap and finally create a gap4 database.
    The position of reads in a contig is shown in the phrap_stdout file. How to extract this information is documented in http://www.phrap.org/phredphrap/phrap.html.  The read information in this file does not fit with the read position information obtained from the show relationship view in gap4!  There is often a few bases in difference. Anyone else seen this?
    Best regards,

    • Nobody/Anonymous

      The gcphrap version is  0.990329
      pregap4 is v 1.5
      gap4 is v 4.10
      Best regards,


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