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
