extract_seq - is it broken?

James Bonfield jkb at mrc-lmb.cam.ac.uk
Fri Feb 7 04:49:47 EST 1997

Andy Law wrote:

> >  You need to also use the -clip_cosmid option. This wasn't in earlier
> >  versions of extract_seq. The reasoning is that it's sometimes useful
> >  to keep the cosmid sequence. This is even true in gap4 where leaving
> >  the cosmid sequence in allows you to easily see the cosmid ends and
> >  hence find the correct placement of at least two contigs.
> >  
>If I do split my sequence files in this way, will gap assemble them correctly?

Provided you have the inserts worked out and in separate files gap4 will
assemble them fine. However to make the most of things you may wish to create
experiment files rather than plain text files. You mentioned that you'd
written a script to duplicate the experiments file with fixed names and
sequences. If this is working fine (it's far from trivial if you have quality
cutoff points and, even worse, tagged regions) then gap4 should work ok.

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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