[mira_talk] Re: Scaffolding MIRA results with BAMBUS: a primer
- From: Brian Forde <bforde@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 9 Oct 2009 12:29:50 +0100
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
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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>
>
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"If scientists knew what they were doing they wouldn't call it research"
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