Finally an interesting talk now in this newsgroup! At our lab, we are in
a setup phase playing a little bit around with Staden and the Washington
packages. Concerning Gap4 vs. Consed, I'm a little biased since we
worked more with Gap4.
I have actually a problem by integrating phred in Pregap4:
- Phred -
Thu 27 Jan 13:31:20 2000 phred: phred produced unknown filename:
SCF_fofn.scf_dir/122533a.t3SCF
Renamed file to SCF_fofn.scf_dir/122533a.t3SCF.
can't read "file_id()": no such element in array
while executing
"set file_id($f) $file_id($f2)"
(procedure "phred::run" line 60)
invoked from within
"${mod}::run $files"
(procedure "run_modules" line 14)
invoked from within
"run_modules $files"
invoked from within
"if {!$interactive} {
init_modules
if {[check_modules 1] > 0} {
verror ERR_WARN check_modules \
"One or more modules have not been config..."
(file "/usr/local/staden/linux-bin/pregap4" line 86)
Does someone knows how to solve it?
We tried also the assembler Mira from Bastien Chevreux at DKFZ in
Germany (http://www.dkfz-heidelberg.de/mbp-ased/). It gives also nice
results. Problem is that the output is in CAF format and that one needs
a program caf2gap (Sanger). I had a problem to compile it for Linux. Has
anyone done it so far and succeeded?
regards
Stefan
--
==============================================================================
Stefan Weckx
Laboratory of Molecular Genetics - VIB
Department of Biochemistry
University of Antwerp
Universiteitsplein 1
B-2610 Antwerpen - Wilrijk
Belgium
==============================================================================
James Bonfield wrote:
>> In article <388FBFE5.1065EE90 at mail.ru> Volodya <bo-ba at mail.ru> writes:
> > Thank you very much for your input. What do you think about the use of
> >phred scores in Staden and Consed? I am interested in using that package
> >that allows fuller usage of this objective quality measure, and possibly
> >a lesser human intervention and better integration within the automated
> >system. Are Consed and Staden equivalent in this regard, if they are set
> >up to use phred and phrap? On the other note, is it too much to ask you
> >to send me your perl script? It would be very useful for a quick test
> >drive of Staden/phred/phrap package, since I hear that setting it might
> >be a problem.
>> Hello Volodya,
>> I implemented the use of phred scores within Gap4 so I can explain how
> this works, although I think that the best source of information for
> Gap4 is in the following web pages:
>>http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_121.html#SEC194>http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_122.html>http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_55.html#SEC85>> For what it's worth, the Sanger Centre are now routinely using Gap4 in
> the "confidence" consensus mode to direct their final editing. The
> original estimates showed that this final editing stage was sped up
> around 7 fold (compared to their original strategy of checking all
> discrepancies not automatically fixed by auto-edit) with comparable
> final consensus accuracy.
>> I cannot well explain how this compares to Consed. I have only seen
> consed once, and I didn't use it myself. Indeed we have deliberately
> avoided asking for a copy of Consed to ensure that our ideas are fresh
> (although sometimes the solution is obvious). However from what I gather
> consed cannot calculate a consensus itself. Rather it uses the
> consensus given to it by phrap. Hence the confidence values assigned
> to consensus bases are those that phrap determines. Unfortunately we
> can no longer obtain any newer versions of phrap, so I do not know how
> well the newest versions compare to the release we have (0.960731),
> but I believe the phrap consensus algorithm has been recently changed.
>> 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/
