Hi Matt, You're using our genome-preview site and much of the data on this site, including the HAIB Methyl WGBS data that you're looking at, has not yet been through our QA process. We advise users to be extremely cautious when viewing data on our preview site.
It looks like this track isn't displaying the colors properly in dense mode (the mode it looks like you're viewing the data in). If you change the track visibility to pack or full, you should see the colors. I'll alert our engineers of this bug so that the colors will be displayed properly in dense mode before we release this track to our public site. Actually, when I go to your region, even if full or pack is selected there is too much data to display in pack or full so the browser is automatically showing it in dense. You'll need to zoom into a smaller region before the browser will allow the data to expand into full or pack mode. Once you can see the data in full or pack, you'll see the colors. When I look at this data in pack or full mode, I am seeing that there are additional colors (orange and yellowish-green) not described in the track description page (only red, yellow and green are described). It looks like orange is between red and yellow with regard to % of reads methylated and yellowish-green is between yellow and green, however, I cannot be sure. Since this track is still in development, it is very likely that the description page has not been finished or finalized and that is why it is doesn't yet thoroughly describe the data. To find out what all the colors signify, I recommend contacting the lab using the contact information in the track description. Katrina -------------------------- Katrina Learned UCSC Genome Bioinformatics Group http://genome.ucsc.edu On Wed, Jun 6, 2012 at 3:54 PM, Matt Grimmer <[email protected]> wrote: > I'd like to visualize the H1 and GM12878 Methyl WGBS data from > ENCODE/HudsonAlpha on the Genome Browser. > > The information page describes the traditional green / yellow / red scheme > indicating methylation levels, but the tracks appear in only one color on > the browser (image attached). Is this a mistake in the bigBED display, or > do I have something set incorrectly? > > Any input is much appreciated. Thanks. > > Matt Grimmer > UC Davis Genetics PhD candidate, Farnham Lab > NRT 6514, 1450 Biggy Street. LA, CA 90089 > USC/Norris Comprehensive Cancer Center > Biochemistry & Molecular Biology Dept. > 323-442-7757 lab, 415-692-4824 cell > http://goo.gl/CcgKa > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
