[mira_talk] Re: Scaffolding MIRA results with BAMBUS: a primer
- From: Brian Forde <bforde@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 9 Oct 2009 15:50:43 +0100
Hi Dan,
Thanks for your reply.
read naming scheme is correct XXXXXXXXXXXXXX.f/r where X is some
letter/number
bambus version is 2.33.
On Fri, Oct 9, 2009 at 1:00 PM, Dan Bolser <dan.bolser@xxxxxxxxx> wrote:
> 2009/10/9 Brian Forde <bforde@xxxxxxxxx>:
> > I have a bambus related question if some one has the time to answer it.
> >
> > I am trying to use bambus to generate scaffolds from my 454 mate -pairs
> (3kb
> > library) but always get the same amount of scaffolds as contigs. I assume
> > that this is a problem with my mates file but have no idea how to fix it.
> >
> > Library threeKB 700 3000 (..............).*
> > pair (.*)\.f (.*)\.r
> >
> > all values are separated by tabs. I know its not a bambus help list but
> some
> > ppl seem to have had great success with producing scaffolds
>
> I assume that the regular expressions above fit the read naming
> convention in your mate pairs?
>
> Again it's off topic, but which version of Bambus are you using? I did
> some tests where I inserted a few wrong mate-pairs into an otherwise
> perfect set of scaffolding mates, and the result was a 'catastrophic
> failure' of the scaffolding algorithm. Apparently there is a new
> version, but I haven't had the chance to test it yet.
>
>
>
> > Thanks in advance
> >
> > Brian
> >
> > On Tue, Sep 1, 2009 at 7:31 AM, Martin A. Hansen <mail@xxxxxxxxx> wrote:
> >>
> >> That does indeed look very useful!
> >>
> >>
> >>
> >> Martin
> >>
> >>
> >> On Tue, Sep 1, 2009 at 12:16 AM, Bastien Chevreux <bach@xxxxxxxxxxxx>
> >> wrote:
> >>>
> >>> Dear all,
> >>>
> >>> Gregory Harhay from the USDA has written an excellent primer on how he
> >>> uses
> >>> BAMBUS to scaffold MIRA results. I'll distribute it along the next
> >>> releases,
> >>> in the mean time you can find it in the online "Manuals" section on the
> >>> MIRA
> >>> website:
> >>> http://www.chevreux.org/mira_manuals.html
> >>>
> >>> He shows an example for how to do it with a 25kb paired-end library.
> >>> Adapting
> >>> to other library sizes or for projects with different library sizes
> >>> should be
> >>> doable with a bit of reading manuals (MIRA & BAMBUS) :-)
> >>>
> >>> This is the first third-party documentation received (yay!) and I'd
> like
> >>> to
> >>> thank Greg wholeheartedly for this as I know it'll help out a few
> people.
> >>>
> >>> Best,
> >>> Bastien
> >>>
> >>> PS: In other news, the final release of MIRA 3 is being delayed by
> >>> something I
> >>> don't know whether it's a true memory leak or memory fragmentation
> eating
> >>> up
> >>> available memory. The joys of millions of reads ... *sigh*
> >>>
> >>> --
> >>> You have received this mail because you are subscribed to the mira_talk
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> please
> >>> visit http://www.chevreux.org/mira_mailinglists.html
> >>
> >
> >
> >
> > --
> > "If scientists knew what they were doing they wouldn't call it research"
> >
>
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--
"If scientists knew what they were doing they wouldn't call it research"
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