Hi Chuck, At the moment, I'm seeing an error when I try to load the track hub:
ERROR: Unsupported type 'bigWigd' in hub This appears to be a typo on the S7 trackDb definition . . . "type bigWigd" should be "type bigWig". That might be responsible for S7 showing up in an odd place. If fixing the typo doesn't fix the display problems, you can also take a look at the "visibility" and "priority" settings for trackDb. We are working on documenting all of the settings relevant to track hubs, and the work-in-progress is on our preview machine (keep in mind that some of this could change): http://genome-preview.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html Visibility is described under "Common trackDb settings" and priority under the "Common, though less frequently used settings" section. Regarding your questions: > 1. Would such a url be stable over long periods such that it can be > included a published pdf? Yes, that is our intent. Track Hubs were developed to provide a stable way for users to host and display their own data in the Genome Browser, without any of the data being stored at UCSC, where it would be subject to our expiration policies. If we change or add trackDb settings in the future, we plan to continue to support settings for existing track hubs so that they will continue to function as intended. > 2. Can you instruct me how to create such a url if for example I > wanted to reduce the pixel with to 1400? You can set the pixel width by adding &pix=1400 to the url. If you leave the setting out, pixel width is determined by a user's current pixel width setting. If there is no such setting in a user's cart, it is determined by the width of a user's web browser when the URL is clicked. Even though it is possible to set pixel width via the url, there is not support for changing all browser settings in a track hub (akin to the "browser" lines for custom tracks) yet. Adding a mechanism for changing browser settings in track hubs is on our task list. I hope this is helpful! If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 7/10/12 4:20 PM, chuck wrote: > Pauline: > > Thanks for spotting the bug. > > I did fix it. > > When went to the url you provided below everything looks OK, save the > S7 is now at the top (instead of being in order between S6 and S8) > and the left label "S7" appear to be right justified unlike the > rest. > > And some tracks were not displayed. > > ______- > > 2 Questions: > > 1. Would such a url be stable over long periods such that it can be > included a published pdf? > > 2. Can you instruct me how to create such a url if for example I > wanted to reduce the pixel with to 1400? > > > _______________________ > > > here is a session with the relevant settings. But the S7 label is > still to the right. > > Here is a UCSC browser session I'd like to share with you: > http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Charles%20H.%20Langley&hgS_otherUserSessionName=50genomes_10July2012_1 > > Thanks, Chuck > > > On 10 Jul 2012, at 10:26, Pauline Fujita wrote: > >> Hello Chuck, >> >> It appears you have an error in your hub. The track >> win.s2.bg3s2.200bp.jkh.rm.chr3.s11.0s.reduced.cluster.7.bw appears >> twice in your trackDb.txt file. If you fix this, then the following >> URL should work to get you to the main browser display with your >> hub loaded. You'll want to make sure that you have the track >> visibilities set to how you want them: >> >> http://genome.ucsc.edu/cgi-bin/hgTracks?db=dm3&hubUrl=http%3A%2F%2Frooted1.ucdavis.edu%2F~chuck%2Fgbtrx%2Fdpgp1_TrackHub%2Fhub.txt >> >> >> >> Best regards, >> >> Pauline Fujita UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu > > > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
