[mira_talk] Re: Scaffolding

HI Brian:

It¹s be  a while since I ran  Bambus , so take what I say with a grain of
salt.  I¹ll be re-analyzing some paired-end 454 data with BAMBUS in the near
future, and I promise to document these steps  and send them out to this
list. 

You are right in focusing in on the .mates file, but the library naming
scheme is a bit more complicated than just the sff file name.

1)  BAMBUS requires fasta input sequences, not sff seqs. Use sff_extract.
2)  Our read names went something like FEQEWE00123.f or FEQEWE00123.r (
forward and reverse respectively) where the library name is FEQEWE this is
critical to get properly specified in the .mates file , (......).*
3)  I remember I need to specify a bambus.conf too

That all I¹ve got right now. Hope this helps.

Greg


On 6/4/09 9:13 AM, "Brian Forde" <bforde@xxxxxxxxx> wrote:

> Hi Bastien,
> 
> No rush with the scaffolding just a query.
> 
> Thanks Gregory. Regarding bambus can  you use it for 454 reads. I'm currently
> trying to get it to work for my reads but am having some trouble. I believe
> it's with my .mates file. Does library name refer to the 454 sff file name?
> 
> cheers
> 
> Brian
> 
> On Thu, May 28, 2009 at 8:15 PM, Gregory Harhay <gregory.harhay@xxxxxxxxxxxx>
> wrote:
>> We've had pretty good luck using BAMBUS to scaffold our paired-end reads.
>> 
>> http://amos.sourceforge.net/docs/bambus/
>> 
>> Greg
>> 
>> 
>> On 5/28/09 1:52 PM, "Bastien Chevreux" <bach@xxxxxxxxxxxx> wrote:
>> 
>>> > On Montag 18 Mai 2009 Brian Forde wrote:
>>>> >> Is there any Scaffolding tool built into Mira? I am assuming not
>>> >
>>> > hi Brian,
>>> >
>>> > no, currently not. Most users so far had their own scaffolding routines or
>>> use
>>> > other software, but I start to receive more and more questions regarding
>>> > scaffolding. I have it now on my TODO, but currently no idea when I could
>>> > implement that.
>>> >
>>> > Regards,
>>> >   Bastien
>>> >
>> 
>> 
>> 
>> 
>> 
>> 
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> 
> 

Gregory P. Harhay, PhD
Computational Biologist
Animal Health Research Unit
USDA-ARS-Roman L. Hruska  U.S. Meat Animal Research Center
Clay Center, NE 68933
v - 402.762.4250

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