Re: [AMOS-help] Make-consensus

[Adam P. <aph...@gm...>]

OK, great. Layout records are identical to contig records, but without
consensus sequence and quality values. You should be able to recall the
consensus by converting all the contig records into layout records. Try the
following commands:
> bank-report -b your.bnk | sed 's/^{CTG/{LAY' > new.afg
> bank-transact -m new.afg -b new.bnk -c
> make-consensus -B -b new.bnk

If all goes as planned, this will convert all your existing contig (CTG)
records to layout records (LAY), recall the consensus, and insert new contig
records into new.bnk. AMOS should ignore the unexpected seq and qual records
in the "faked" layout records. Let me know if you run into any problems.

Good luck,
-Adam


On Tue, Aug 5, 2008 at 6:16 PM, Tobias Rausch <ra...@mi...>wrote:

> Hello Adam,
>
> Thanks for the quick response.
> I have a CTG record with the gapped consensus
> and all the TLE records (read offset, clear range, etc.).
> I would like to convert these contig records into layout records and then
> run make-consensus.
> I managed to use my test.afg file to create a "bank" but I don't know how
> to create a tig-file.
>
> Thanks, Tobias
>
>
> -----Ursprüngliche Nachricht-----
> Von: Adam Phillippy [mailto:aph...@gm...]
> Gesendet: Di 8/5/2008 10:43
> An: Tobias Rausch
> Cc: amo...@li...
> Betreff: Re: [AMOS-help] Make-consensus
>
> Hello Tobias,Do you have full contig records in your afg file? If so you
> could convert these into AMOS layout records which could then be passed to
> make-consensus. The layout record is nearly identical to the contig record,
> so the conversion would be easy. Otherwise, there is a simple layout format
> you could generate that make-consensus accepts with the -S option. Let me
> know if you have CTG records in the afg file and I can explain how to
> proceed.
>
> Best,
> Adam
>
>
> On Tue, Aug 5, 2008 at 11:58 AM, Tobias Rausch <ra...@mi...
> >wrote:
>
> > Hello,
> >
> > I am using Hawkeye and I already have an AMOS message file *.afg.
> > I want to realign the reads with the make-consensus tool.
> > Since I already have approximate layout positions of the reads in the
> > afg file I want to bypass the overlapper and tigger. Unfortunately,
> > make-consensus requires a tig-file.
> >
> > ./amos-2.0.4/bin/make-consensus  <tig-file> <bank-name>
> >
> > Is there an easy way to generate such a tig-file out of an *.afg file
> > with placed reads?
> >
> > Thanks,
> > Tobias
> >
> >
> > -------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Moblin Your Move Developer's
> > challenge
> > Build the coolest Linux based applications with Moblin SDK & win great
> > prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the
> world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > _______________________________________________
> > AMOS-help mailing list
> > AMO...@li...
> > https://lists.sourceforge.net/lists/listinfo/amos-help
> >
>
>