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gcphrap and gap4 bug

  • 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  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,

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