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 > > > > > > > > > -- > You have received this mail because you are subscribed to the mira_talk > mailing list. For information on how to subscribe or unsubscribe, please > visit http://www.chevreux.org/mira_mailinglists.html > > > > > 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 > > > -- "If scientists knew what they were doing they wouldn't call it research"