Work at SourceForge, help us to make it a better place! We have an immediate need for a Support Technician in our San Francisco or Denver office.

Close

gcphrap and gap4 bug

2006-07-18
2013-04-18
  • 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,
    Peter

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