[mira_talk] Re: Scaffolding
- From: Brian Forde <bforde@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 5 Jun 2009 13:15:31 +0100
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:
>
> It’s be a while since I ran Bambus , so take what I say with a grain of
> salt. I’ll 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 I’ve 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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