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 >>>>> > >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> 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 >> >> > > 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