Hi Federico, Thank you for clarifying. It actually looks like you are trying to create what we call a "Container Track" (which is very closely related to a composite track). I think you just need to add one setting, noInherit On, to the container trackDb entry like so:
track ChromStatehg19 container multiWig noInherit On shortLabel ChromState_hg19 longLabel ChromState_hg19 various Histone Mods type bigWig 0.00 700 viewLimits 0.00 500 configurable on visibility full maxHeightPixels 100:30:11 showSubtrackColorOnUi on aggregate transparentOverlay priority 1 From the "Composite Track" section of the http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/README: To include a subtrack of a different type, specify the complete settings for the subtrack type, and use the "noInherit on" trackDb setting. NOTE: This is required for "Multi-View" (see below). We will be adding this note to the "Container Track" section of the trackDb/README. I hope this is helpful! Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Federico De Masi wrote, On 05/04/11 06:23: > Hi Luvina, > > sorry for being "confusing" and a newbie. Finally realised that what I > want is a composite track (?), just like (http://snipurl.com/27t075) > http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=194098509&c=chrX&g=wgEncodeReg > > I have several tracks from separate experiments which I would like to > avoid taking most of the space in the browser, thus I would love to use > the "aggregate" function. > > My tables are properly created, as I can see the tracks succesfully > showing up in the browser. Still, when I copy the example from the > how-to you directed me to, and load it as a new "recompiled" trackDb > table, I do not see the overlay/aggregate feature, but all tracks > visible as usual, as if nothing ever happened. > > I am sure it's something very simple, but can't see it. > > Thanks for the help. > > ========= trackDb.ra section============== > track ChromStatehg19 > container multiWig > shortLabel ChromState_hg19 > longLabel ChromState_hg19 various Histone Mods > type bigWig 0.00 700 > viewLimits 0.00 500 > configurable on > visibility full > maxHeightPixels 100:30:11 > showSubtrackColorOnUi on > aggregate transparentOverlay > priority 1 > > track hASC_WCE > shortLabel hASC_WCE > longLabel ChIP-seq data 1 from Litterature > parent ChromStatehg19 > type bigWig 0.00 200 > color 255,212,128 > > track hASCt1_CTCF > shortLabel hASCt1_CTCF > longLabel ChIP-seq data 2 from Litterature > parent ChromStatehg19 > type bigWig 0.00 600 > color 255,100,50 > > track hASCt2_CTCF > shortLabel hASCt2_CTCF > longLabel ChIP-seq data 3 from Litterature > parent ChromStatehg19 > type bigWig 0.00 600 > color 100,150,128 > > ======================================== > On 03/05/2011 19:11, Luvina Guruvadoo wrote: > >> Hi Frederico, >> >> From your email, I wasn't sure if you are trying to create super tracks >> (as suggested by your subject and first paragraph) or composite tracks >> (as suggested by your sample trackDb entry). Please see the following >> link for descriptions and also instructions on how to create trackDb >> entries for each: >> http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/trackDb/README. >> (the 'SuperTracks', 'Composite Tracks' and '18. type bigWig' sections >> should be useful for you). Information about adding bigWigs to the >> browser can be found here: >> http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.trackDb. >> >> Also, here are examples of a composite track: >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=193917389&c=chr21&g=wgEncodeMapability, >> and super track (this one contains several composite tracks, but please >> note that super-tracks can also contain non-composite tracks): >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=193917389&c=chr21&g=wgEncodeDNAseSuper >> >> >> If you are trying to create a composite track, I noticed that in the >> subtrack blocks your sample trackDb entry, you are missing values for >> the shortLabels and longLabels of your subtracks. Also, be sure that you >> are following the database loading procedure for bigWigs described in >> the '18. type bigWig' section of the first link above. You should end up >> with tables entitled NAME2 and NAME3, each with a single row pointing to >> the location of that subtracks' bigWig file in your file system. You >> shouldn't have a NAME table. >> >> If you have any further questions after reading the documentation, >> please contact us again at [email protected]. >> >> --- >> Luvina Guruvadoo >> UCSC Genome Bioinformatics Group >> >> >> Federico De Masi wrote: >> >>> Dear Colleagues, >>> >>> I have been setting up a local UCSC browser for our own purposes and >>> have been trying to consolidate similar tracks together, such as for >>> the Encode supertracks. >>> >>> No matter what I have tried, copying from the available information, I >>> do not manage to get the system to work. >>> >>> Here's an example of my trackDb.ra entry >>> >>> track NAME >>> compositeTrack on >>> type bigWig 0.00 700 >>> shortLabel BLAH >>> longLabel LONG BLAH >>> priority 0 >>> group GRP >>> >>> track NAME2 >>> subTrack NAME >>> shortLabel >>> longLabel >>> priority 1 >>> >>> track NAME3 >>> subTrack NAME >>> shortLabel >>> longLabel >>> priority 2 >>> >>> When I insert this into trackDB (together with other tracks), I get >>> the tracks NAME, NAME2 and NAME3 created. Yet, I see NAME2 and NAME3 >>> as separate tracks in the browser and no signs of life from NAME. >>> I have tried to generate a bigWig table called NAME where I have 2 >>> records pointing at the bw files NAME2 and NAME3. >>> I now see that track space in the browser, but empty. And, still, both >>> NAME2 and NAME3 tracks. >>> >>> How can I put NAME2 and NAME3 "inside" name? It is evident that by >>> just adding the code in the .ra file adding that to the trackDb table >>> is not enough. >>> >>> Can someone please point me into the right direction? >>> >>> Thanks, >>> >>> Federico De Masi, PhD, >>> Assistant Professor >>> The Technical University of Denmark - DTU >>> Center for Biological Sequence Analysis - CBS >>> Kemitorvet 208/002 >>> DK-2800 KGS. LYNGBY, DENMARK >>> Telephone: (+45) 45 25 24 21 >>> Fax: (+45) 45 93 15 85 >>> http://www.rg.cbs.dtu.dk >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
