assemble_shotgun... assemble4 ...BUG?

[jkb at mrc-lmb.cam.ac.uk]

In <1044846189.3e47166d1899b at imap-genome.wi.mit.edu> major at genome.wi.mit.edu writes:

> My question is:  How can I get assemble_shotgun to behave like the
> Assembly->Normal Shotgun Assemble feature in the GUI?  Why does assemble_shotgun
> not appear to manipulate sequence in the files it is given when the GUI Normal
> Shotgun Assembly does? 

Note that the Assembly->Normal Shotgun Assemble is the same thing as
assemble_shotgun. It's probably just a matter of options, and some of the
default options may not be particularly sensible.

Take a look at $STADENROOT/lib/gap/auto_assemble.tcl and the OK_Pressed1
function. This calls assemble_shotgun, so you could shove a puts in there to
see what arguments it is using.

James
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Fax: (+44) 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
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Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/