In <3A40C7D4.A16BC909 at ircm.qc.ca> Johanne Duhaime <duhaimj at ircm.qc.ca> writes:
>> I tried to use staden package for assembly.
>> I first run pregaps and get the files exp created from my scf files.
>> Then I use gap4. Create a new database, go to Assembly/ Directed
> assembly/ and select all the exp files created. Then I keep having the
>> directed_assembly: no AP line in 'file name'
>> What am I doing wrong?
Using directed assembly! :-)
Try using Normal Shotgun Assembly. Directed assembly assumes that all
experiment files have an assembly position (AP) marker indicating the rough
location in the final assembly - ie it can be used for importing phrap, fakii,
cap3, etc data.
James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/