[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 13:00:16 +0100
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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>>
>
>
>
> --
> "If scientists knew what they were doing they wouldn't call it research"
>
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