Working with pregap4+phrap, if I'm not wrong, the .ace file output should be obtained passing the flag option -ace (or -new_ace) as phrap argument through the "phrap assembly" module in pregap4. I get no such output, as well as other outputs like .view.
How can I obtain the .ace format of my assemblies?
Thanks a lot for any help..
Dpt. Plant Biology and IPP-CNR
University of Turin
V.le P.A. Mattioli, 25
Pregap4's interface to Phrap is via experiment files. It assumes the output will be exp too so Gap4 or Pregap4 can import it. If you wish to assemble with ace output then you'd be best stopping before the phrap bit and run phrap (gcphrap) on the command line with -ace.
I have a consed ace file with polymorphism tags from polyphred. This I would like to convert to a gap4 database.
I looked at the phrap2caf and caf2gap but the major problem is that the caftools drop all consensus tags (which I have from polyphred).
Before diving deeper into the caftools I just wanted to ask, if there is another solution.
Not that I know of. I don't think CAF supports consensus tags well (or at all).
I think baylor may have created a consed<->gap conversion tool (both ways), but I'm not sure what ever came of it or even if I remember the correct centre.