Hi, I am updating and adding all the scripts required to update biodb2 resources in my git branch, nkim/biodb2_update
Namshin Kim On Fri, Jul 17, 2009 at 11:09 AM, Namshin Kim <deepr...@gmail.com> wrote: > Hi, > > Here is a list of MULTIZ files I'd downloaded. I am going to reorganize > scripts and make ucsc_update branch, so that anybody can update. > > braFlo1_multiz5way ce6_multiz6way oryLat2_multiz5way > sacCer1_multiz7way > ce4_multiz5way hg18_multiz44way petMar1_multiz6way > xenTro2_multiz7way > > Yours, > Namshin Kim > > > > > On Thu, Jul 16, 2009 at 1:35 PM, Namshin Kim <deepr...@gmail.com> wrote: > >> Hi, >> Now that we have additional 2.5TB space in biodb2, it is time to make >> pre-built NLMSA for newly updated MAF/axtNet. I am building multiz44way >> first. Let's make some plans... >> >> Yours, >> Namshin Kim >> >> >> >> >> On Tue, May 26, 2009 at 6:39 PM, Namshin Kim <deepr...@gmail.com> wrote: >> >>> Hi Kenny, >>> For SGD, I suggest we make SGD category in worldbase. Currently, all the >>> genome assemblies are in worldbase.Bio.Seq.Genome, but we can make another >>> category for SGD like worldbase.SGD.Seq.Genome.YEAST.xxxx >>> >>> In order to provide all in UCSC genome browser, we need to make a list of >>> URLs for genomes, MAF files, axtNet files, liftOver, and etc. 2bit files >>> need to be processed separately to make fasta sequences. >>> >>> How would you like to proceed? >>> >>> Yours, >>> Namshin Kim >>> >>> >>> On Tue, May 26, 2009 at 2:59 PM, Kenny Daily <kmda...@gmail.com> wrote: >>> >>>> >>>> I'd like to help too...possibly also with some non-UCSC genomes? For >>>> example, yeast biologists (at least the ones I work with) only use >>>> SGD, not UCSC. UCSC's genome build for sacCer is reaaaallllyyy out of >>>> date, and isn't compatible with SGD, where the rest of the annotation >>>> data of interest is. This also means that the alignment is out of date >>>> as well, which I rebuilt as well with TBA, not Multiz. I could >>>> definitely share this data as well. >>>> >>>> Kenny >>>> >>>> On May 25, 6:32 pm, Christopher Lee <l...@chem.ucla.edu> wrote: >>>> > Hi Namshin, >>>> > Thanks! It took much longer than Marek and I wanted, but a much >>>> > bigger disk (2 TB?) has been installed there by the folks who support >>>> >>>> > that machine. Marek knows the details. >>>> > >>>> > -- Chris >>>> >>>> >>>> >>> >> > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
