[mira_talk] Re: Scaffolding

Brian:

Great!  Glad to hear  that it is working for you. The instructions with
supplied with the software are a bit impenetrable in places.

Greg


On 6/5/09 7:15 AM, "Brian Forde" <bforde@xxxxxxxxx> wrote:

> Thanks Gregory.
>  I have it working now.
> 
> regards
> 
> Brian
> 
> 
> On Thu, Jun 4, 2009 at 9:28 PM, Gregory Harhay <gregory.harhay@xxxxxxxxxxxx>
> wrote:
>> 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 <http://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
>>> <http://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
>>>> <http://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
>> 
>> 
> 
> 

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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