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
>
--
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
