[mira_talk] Re: Scaffolding MIRA results with BAMBUS: a primer
- From: Dan Bolser <dan.bolser@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 9 Oct 2009 17:36:16 +0100
Yeah, looks right.
All I can suggest is asking the same question on the SEQanswers forum.
Dan.
2009/10/9 Brian Forde <bforde@xxxxxxxxx>:
> 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*
>> >>>
>> >>> --
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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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