Hi Dwight, Yes, it would be best to set up a mirror and then create an assembly for S pombe.
Here is some information on mirroring the genome browser: http://genome.ucsc.edu/admin/mirror.html http://genomewiki.ucsc.edu/index.php/Browser_Mirrors If you decide you want a minimal or partial mirror you can read about that here: http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation Here is some information on creating a new assembly: http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database Another helpful resource is the mailing list archive of our [email protected] list. You can search the archives from here: http://genome.ucsc.edu/contacts.html Katrina Learned UCSC Genome Bioinformatics Group Dwight Kuo wrote, On 10/01/10 11:34: > Hi > > Thanks. I was wondering if it's possible to add sequences and annotation for > S pombe? Would it be easier to build a local installation of the genome > browser? > > Thanks, > > D > > > > On Thu, Sep 30, 2010 at 16:17, Vanessa Kirkup Swing > <[email protected]>wrote: > > >> Dear Dwight, >> >> You are using sacCer2 which uses roman numerals for the chromosomes. If you >> use sacCer1, it works fine. If you go to: >> http://genome.ucsc.edu/cgi-bin/hgGateway >> >> and click on the "sequences" link it will list the chromosome names for the >> database and assembly you are interested in. >> >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> ----- Original Message ----- >> From: "Dwight Kuo" <[email protected]> >> To: "Vanessa Kirkup Swing" <[email protected]> >> Cc: "genome-www" <[email protected]> >> Sent: Thursday, September 30, 2010 3:53:00 PM GMT -08:00 US/Canada Pacific >> Subject: Re: UCSC Genome Browser bedGraph format >> >> Hi Vanessa, >> >> >> I'm currently inputting: >> >> >> >> track type=bedGraph >> chr1 2000 2300 3.0 >> >> >> into the S.cereivisae genome from >> http://genome.ucsc.edu/cgi-bin/hgCustom >> >> >> D >> >> >> >> >> On Thu, Sep 30, 2010 at 15:51, Vanessa Kirkup Swing < [email protected]> >> wrote: >> >> >> Hi Dwight, >> >> Can you tell me what database and assembly you are using? Also, are you >> using our site: http://genome.ucsc.edu/cgi-bin/hgCustom or are you using a >> mirror? >> >> Thanks! >> >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> ----- Original Message ----- >> >> >> >> From: "Vanessa Kirkup Swing" < [email protected] > >> To: "Dwight Kuo" < [email protected] > >> Cc: "genome-www" < [email protected] > >> Sent: Thursday, September 30, 2010 3:16:21 PM GMT -08:00 US/Canada Pacific >> Subject: Re: UCSC Genome Browser bedGraph format >> >> Hi Dwight, >> >> This works for me on on for the human hg18 assembly. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> ----- Original Message ----- >> From: "Dwight Kuo" < [email protected] > >> To: "Vanessa Kirkup Swing" < [email protected] > >> Sent: Thursday, September 30, 2010 3:07:16 PM GMT -08:00 US/Canada Pacific >> Subject: Re: UCSC Genome Browser bedGraph format >> >> I tried that before. Actually I'm trying something even simpler: >> >> >> >> track type=bedGraph >> chr19 59302000 59302300 -1.0 >> chr19 59302300 59302600 -0.75 >> chr19 59302600 59302900 -0.50 >> chr19 59302900 59303200 -0.25 >> chr19 59303200 59303500 0.0 >> chr19 59303500 59303800 0.25 >> chr19 59303800 59304100 0.50 >> chr19 59304100 59304400 0.75 >> chr19 59304400 59304700 1.00 >> >> >> >> On Thu, Sep 30, 2010 at 14:59, Vanessa Kirkup Swing < [email protected]> >> wrote: >> >> >> Dear Dwight, >> >> The example that you are referring to is from this page: >> >> http://genome.ucsc.edu/goldenPath/help/bedgraph.html >> >> There is a note that says "if you copy/paste the above example, you have to >> remove the carriage returns." >> >> If you do this, it should work. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> >> >> >> ----- Original Message ----- >> From: "Dwight Kuo" < [email protected] > >> To: [email protected] >> Sent: Thursday, September 30, 2010 1:39:16 PM GMT -08:00 US/Canada Pacific >> Subject: UCSC Genome Browser bedGraph format >> >> When I try to input the UCSC Genome Browser's examples for bedGraph format, >> i.e.: >> >> >> >> browser position chr19:59302001-59304701 >> browser hide all >> browser pack refGene encodeRegions >> browser full altGraph >> # 300 base wide bar graph, autoScale is on by default == graphing >> # limits will dynamically change to always show full range of data >> # in viewing window, priority = 20 positions this as the second graph >> # Note, zero-relative, half-open coordinate system in use for bedGraph >> format >> track type=bedGraph name="BedGraph Format" description="BedGraph format" >> visibility=full color=200,100,0 altColor=0,100,200 priority=20 >> chr19 59302000 59302300 -1.0 >> chr19 59302300 59302600 -0.75 >> chr19 59302600 59302900 -0.50 >> chr19 59302900 59303200 -0.25 >> chr19 59303200 59303500 0.0 >> chr19 59303500 59303800 0.25 >> chr19 59303800 59304100 0.50 >> chr19 59304100 59304400 0.75 >> chr19 59304400 59304700 1.00 >> >> >> This fails, with the message "Error Unrecognized format type=bedGraph line >> 10 of custom track" >> >> >> Sincerely, >> >> >> Dwight >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
