extract_seq - is it broken?

Andy Law Andy.Law at bbsrc.ac.uk
Mon Feb 10 04:49:48 EST 1997


In article <9702070950.AA05925 at arran>, jkb at mrc-lmb.cam.ac.uk (James
Bonfield) wrote:

 >  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. 

What I had intended doing was the following. Each sequence is an
ABI-derived trace file. I can see within that file that there are
restriction sites that may indicate multiple inserts. Since I want the
information from the traces to be available for each insert, but each
insert needs to be assembled separately, I figured the best way to do it
would be to let pregap run on the file as normal. Then, having generated a
single experiment file to encompass the whole sequence, I would duplicate
the experiment file, modifying the reading name slightly (readings A and B,
for example) and adding a CS or similar tagging line to each to mask out
the non-required sequence. Both experiment files would point to the same
template, clone, and (more importantly) trace file. Since each points to
the same file, the cut-offs should remain the same. Will *that* work?

Andy Law
------------------
( Andy.Law at bbsrc.ac.uk )
( Big Nose in Edinburgh )



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