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