Wednesday, February 13, 2013

grouping multiWig as subtracks

This is not a tip, but a request (to a UCSC genome feature).

I was trying to set multiWig containers as a subtrack of a composite (as below), but it does not work.

track CAGE
compositeTrack on
shortLabel CAGE
longLabel CAGE Tracks
type bed 3
visibility full
priority 20
subGroup1 view Views SGuniq=Signal_Uniqmap SGall=Signal_Allmap
subGroup2 stage Stage 10dpp=10dpp 20dpp=20dpp
subGroup3 treatment treatment wt=Wild_Type
dimensions dimensionX=treatment dimensionY=stage
sortOrder stage=+ treatment=+ view=+
dragAndDrop subTracks
configurable on

track CageUniqmapsignal
shortLabel Signal
view SGuniq
type bigWig
autoScale on
alwaysZero on
windowingFunction maximum
maxHeightPixels 50:50:11
parent CAGE

# --------- 10dpp ---------
track 10dpp_wt_CAGE_uniq
container multiWig
shortLabel CAGE_uniq
longLabel 10dpp_wt_CAGE_uniq
aggregate transparentOverlay
showSubtrackColorOnUi on
subGroups view=SGuniq stage=10dpp treatment=wt
parent CAGE

parent 10dpp_wt_CAGE_uniq
color 0,0,255 

track 10dpp_wt_CAGE_uniq.minus
parent 10dpp_wt_CAGE_uniq
color 255,0,0
# --------- tracks for other stages... ---------

Just found that UCSC has not implemented it yet. Here is the message:

"It is not currently possible to combine bigBeds and bigWigs into a multiWig
track. They can be combined into a multiple view composite. The bigWigs
could be combined into a multiWig, but that multiWig cannot itself be part
of a composite. The bigWigs could be displayed both in a multiWig and as
subtracks of a separate composite that also contains bigWigs.

In the future there may be a "container" like multiWig that will contain
both bigBeds and bigWigs. Separately, in the future we may support a
multiWig as one subtrack of a composite. However, neither of these is
currently supported."

Hope this can be implemented soon!!!

(If anyone has a solution to the problem, please let me know. Thanks very much)

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