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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?
The gcphrap version is 0.990329
pregap4 is v 1.5
gap4 is v 4.10