From pregap4 to gap4: exp files

jkb at mrc-lmb.cam.ac.uk jkb at mrc-lmb.cam.ac.uk
Tue Jan 2 06:58:32 EST 2001


In <3A40C7D4.A16BC909 at ircm.qc.ca> Johanne Duhaime <duhaimj at ircm.qc.ca> writes:

> Bonjour
> 
> 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
> following:
> 
> 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
--
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/






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