Hi Federico, Just one more clarification: right now we only have one type of container track, multiWig, which is what you are creating.
Thanks! Katrina Katrina Learned wrote, On 05/04/11 12:13: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
