Hi Hiram, Thanks for your reply. So I was able to get MAF files for our alignment, but now I am trying to figure out how to put those files into the database. We do have a local installation, and I have access to the mysql database. I can't seem to find any instructions or posts that detail how to do it, though. I mean, which tables do I need to create, how do I link the existing reference genome tables, and which of the fields in the MAF file need to be parsed into which tables. Is there a webpage somewhere that tells me how to do this? As always, any help is highly appreciated. Thanks!
- Nik. Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center University of California, Davis Davis, CA http://bioinformatics.ucdavis.edu Hiram Clawson wrote: > Good Evening Nikhil: > > The genome browser only displays bases of the other genome when > you have an alignment. The coordinate basis of the genome > browser is the underlying assembly that the browser is built > upon. If you want a different genome to be compared to that > reference genome, you need to do an alignment. I assume that > is what you have in the axt files. There is a kent source > program axtToMaf that can convert that to maf. > > For an example display of other genomes on a reference genome, > here are 44 genomes displayed in reference to the human genome: > > http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=Nikhil_Joshi > > > > That track is currently set to display bases that are identical as dots . > > Even better, you appear to be talking about an instance of the genome > browser that is local to you and under your control. In that case, > you can load your MAF file as a table in the database of your > reference genome, then the track can appear as does my example > above. > > --Hiram > >> time on the browser page, and then when I drill down to the bases, I >> would see a reference genome for BOTH assemblies. How do I get the >> database to recognize that when I load the Thaliana assembly, I also >> want to load the Arenosa assembly as a separate track in the same >> browser view? Any help would be highly appreciated. Thank you! >> >> - Nik. >> >> Nikhil Joshi >> Bioinformatics Programmer >> UC Davis Genome Center >> University of California, Davis >> Davis, CA >> http://bioinformatics.ucdavis.edu >> >> >> >> Hiram Clawson wrote: >>> If you have an alignment of your contigs to the reference assembly, >>> use the MAF file from that alignment and load that up as a custom >>> track. >>> >>> Or, create a local database for your organism: >>> http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database >>> >>> --Hiram >>> >>> Nikhil Joshi wrote: >>>> I have bunch of contigs created using a velvet assembly, which I am >>>> able to display as a custom track on our local installation of the >>>> genome browser. However, I want to be able to see the actual bases >>>> on the contigs when I drill down to the base level. According to >>>> this post: >>>> http://www.soe.ucsc.edu/pipermail/genome/2006-April/010344.html >>>> that is not possible. What I'm wondering is if the above post is >>>> actually correct, and that it is NOT possible to see bases using a >>>> custom track. And if so, then is it possible to view bases on our >>>> contigs by putting them as a permanent track on our local >>>> installation? Keep in mind that the idea is to have each contig on >>>> a separate line, but when you drill down to the base level, instead >>>> of seeing a solid bar (which is what I have now), you would see the >>>> actual bases. Is this possible, and if so, how do I do it? >>>> >>>> Nikhil Joshi >>>> Bioinformatics Programmer >>>> UC Davis Genome Center >>>> Davis, CA > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
