You would need to change these things for your own project.
Let's use VizHub II as an example: If you don't have wget or curl to run from the commandline, you can simply type it into your browser and then cut and paste text. wget http://vizhub.wustl.edu/VizHub/RoadmapRelease2.txt hub VizHub shortLabel Roadmap Epigenomics Release II at Wash U VizHub longLabel Roadmap Epigenomics Human Epigenome Atlas Release II, VizHub at Washington University in St. Louis genomesFile genomes2.txt email [email protected] wget http://vizhub.wustl.edu/VizHub/genomes2.txt genome hg19 trackDb hg19/trackDb.txt (you can actually have multiple clauses here for each genome) wget http://vizhub.wustl.edu/VizHub/hg19/trackDb.txt (this is actually a large amount of text at 500k). --- track containeredacc2H2BK15ac container multiWig superTrack edaccContainerbyExperiment shortLabel H2BK15ac Summary longLabel EDACC Release II H2BK15ac Summary for 5 sample types type bigWig 0 90000 configurable on visibility hide maxHeightPixels 150:30:11 aggregate transparentOverlay showSubtrackColorOnUi on autoScale on windowingFunction mean priority 1.4 track H1_H2BK15ac_04e bigDataUrl H1_H2BK15ac_04.bigWig shortLabel UCSD H1 H2BK15ac SAK204 longLabel UCSD H1 Cell Line Histone H2BK15ac Library SAK204 EA Release 2 type bigWig 0 90000 parent containeredacc2H2BK15ac color 180,102,255 track H1_H2BK15ac_06e bigDataUrl H1_H2BK15ac_06.bigWig shortLabel UCSD H1 H2BK15ac YL206 longLabel UCSD H1 Cell Line Histone H2BK15ac Library YL206 EA Release 2 type bigWig 0 90000 parent containeredacc2H2BK15ac color 136,102,255 track IMR90_H2BK15ac_K42e bigDataUrl IMR90_H2BK15ac_K42.bigWig shortLabel UCSD IMR90 H2BK15ac SK42 longLabel UCSD IMR90 Cell Line Histone H2BK15ac Library SK42 EA Release 2 type bigWig 0 90000 parent containeredacc2H2BK15ac color 92,102,255 [ ... ] --- So to make a personal hub, find a location where you can store some files and access them via http (or https or ftp). Then create a hub.txt file, a genomes.txt file, and a $db/trackDb.txt file. Put the big* datafiles in there too under $db/ bigDataUrl is a required field for data tracks. Then you can go to the gateway, hgTracks, or Table Browser, click the "track hubs" button, then click the My Hubs tab, and paste in the url to your personal hub. Click add hub, and return to genome browser. -Galt 8/4/2011 11:54 AM, Johnston, Jeffrey: > Hi, > > Are there any examples of how to define these multiWig tracks when using > Track Hubs? It is not clear at all from the Track Hub help page how one > should modify a trackDb.txt file in order to create these kinds of tracks. > > Thanks! > Jeff > > On 8/1/11 5:47 PM, "Greg Roe"<[email protected]> wrote: > >> Hi Chris, >> >> Currently there is no way to upload a custom overlay track (i.e. a >> multiWig). However, we have a new feature called Track Hubs, which allow >> users to create their own sets of tracks remotely and display them in >> the browser. Using Track Hubs, you can display these overlay/multiWig >> tracks. Here's the documentation on Track Hubs: >> >> http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html >> >> You'll want to read the full documentation to set up a hub, but you can >> scan the docs for "multiWig" to see info that pertains to the type of >> tracks you are looking to display. >> >> Please let us know if you have any additional questions: >> [email protected] >> >> - >> Greg Roe >> UCSC Genome Bioinformatics Group >> >> On 8/1/11 11:39 AM, Chris Benner wrote: >>> Hello - >>> >>> Is it possible to create custom "overlap tracks" such the ones produced >>> by >>> the ENCODE consortium? I'm couldn't find any information on the site >>> about >>> making overlap tracks. I'm a huge fan of the Genome Browser and fairly >>> savvy with generating custom tracks, and I (and several others) are very >>> interested in the overlap tracks as a way to more conveniently display >>> information. Thanks in advance, >>> >>> Chris >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
