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 )
