genome browser track order

[Jonathan Rosenski]

Hi,

I am a PhD student at the Hebrew University. I have a question about whether a feature exists.

I have a track hub with composite tracks. I have a specific order that I want the composite tracks to appear, which I have set in my track hub. It is many composite tracks, so dragging to re-order inside the genome browser is not really an option. Whenever I connect the track hub the order comes out alphabetically.

Here is a picture of the genome browser:

and here is a link to the session http://genome-euro.ucsc.edu/s/Tomkap/hg19_track_oder_debug

here is a screen shot of the trackDb.txt

as you can see, Sapenous-Vein-Endothel should come after Aorta-Endothel. But in the browser it comes out alphabetically sorted.

Is there a way to enforce the order as in the trackDb.txt?

[Gerardo Perez]

Hello, Jonathan.

Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.

You can use the priority trackDb setting which will allow you to select the order of tracks within a track group or data hub and will display the order on the browser graphic image. For example, using your trackDb.txt, we can change the order of the st_UXM_Aorta-Endothel-Z0000043G and st_UXM_Saphenous-Vein-Endothel-Z000000RM tracks:

track st_UXM_Aorta-Endothel-Z0000043G
type bigWig
container multiWig
aggregate stacked
showSubtrackColorOnUi on
alwaysZero on
autoScale off
viewLimits 0:1
windowingFunction mean
maxHeightPixels 60:10:5
shortLabel UXM_Aorta-Endothel-Z0000043G
longLabel UXM_stacked_Aorta-Endothel-Z0000043G
parent trackOrder
visibility full
priority 2
...
track st_UXM_Saphenous-Vein-Endothel-Z000000RM
type bigWig
container multiWig
aggregate stacked
showSubtrackColorOnUi on
alwaysZero on
autoScale off
viewLimits 0:1
windowingFunction mean
maxHeightPixels 60:10:5
shortLabel UXM_Saphenous-Vein-Endothel-Z000000RM
longLabel UXM_stacked_Saphenous-Vein-Endothel-Z000000RM
parent trackOrder
visibility full
priority 1

Here is a session that shows this order in the browser graphic image: http://genome.ucsc.edu/s/gperez2/mlq_32261

Here is a link to a UCSC Genome Browser blog post that discusses the priority trackDb setting and other settings that users may find useful: https://genome-blog.soe.ucsc.edu/blog/2022/06/28/track-hub-settings/

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Jonathan Rosenski]

When I put the priority on that level I do not see any difference. It is still alphabetic. Same session. http://genome-euro.ucsc.edu/s/Tomkap/hg19_track_oder_debug

I have also tried putting the priority on the compositeTrack definition but that also did not work.

Here is my example trackDB.txt

########################################################
track st_Endothel
compositeTrack on show
shortLabel Endothel
longLabel Endothel
visibility full

track st_Endothel_super
superTrack on show
parent st_Endothel on
shortLabel Endothel_sup
longLabel Endothel_sup
visibility full


track st_UXM_Aorta-Endothel-Z00000422

type bigWig
container multiWig
aggregate stacked
showSubtrackColorOnUi on
alwaysZero on
autoScale off
viewLimits 0:1
windowingFunction mean
maxHeightPixels 60:10:5

shortLabel UXM_Aorta-Endothel-Z00000422
longLabel UXM_stacked_Aorta-Endothel-Z00000422
parent st_Endothel_super
visibility full
priority 4


track U_track_Aorta-Endothel-Z00000422
bigDataUrl http://www.cs.huji.ac.il/~jrosensk/gb_data_revised/Aorta-Endothel-Z00000422.U.bigwig
shortLabel cU_data_Aorta-Endothel-Z00000422
longLabel Mostly Unmethylated reads proportion
parent st_UXM_Aorta-Endothel-Z00000422 on
type bigWig
viewLimits 0:1
color 0,255,0
visibility full

track X_track_Aorta-Endothel-Z00000422
bigDataUrl http://www.cs.huji.ac.il/~jrosensk/gb_data_revised/Aorta-Endothel-Z00000422.X.bigwig
shortLabel bX_data_Aorta-Endothel-Z00000422
longLabel Other reads (mixed methylation)
parent st_UXM_Aorta-Endothel-Z00000422 on
type bigWig
viewLimits 0:1
color 255,255,0
visibility full

track M_track_Aorta-Endothel-Z00000422
bigDataUrl http://www.cs.huji.ac.il/~jrosensk/gb_data_revised/Aorta-Endothel-Z00000422.M.bigwig
shortLabel aM_data_Aorta-Endothel-Z00000422
longLabel Mostly Methylated reads proportion
parent st_UXM_Aorta-Endothel-Z00000422 on
type bigWig
viewLimits 0:1
color 255,0,0
visibility full

track st_UXM_Aorta-Endothel-Z0000043G
type bigWig
container multiWig
aggregate stacked
showSubtrackColorOnUi on
alwaysZero on
autoScale off
viewLimits 0:1
windowingFunction mean
maxHeightPixels 60:10:5
shortLabel UXM_Aorta-Endothel-Z0000043G
longLabel UXM_stacked_Aorta-Endothel-Z0000043G

parent st_Endothel_super
visibility full
priority 5


track U_track_Aorta-Endothel-Z0000043G
bigDataUrl http://www.cs.huji.ac.il/~jrosensk/gb_data_revised/Aorta-Endothel-Z0000043G.U.bigwig
shortLabel cU_data_Aorta-Endothel-Z0000043G
longLabel Mostly Unmethylated reads proportion
parent st_UXM_Aorta-Endothel-Z0000043G on
type bigWig
viewLimits 0:1
color 0,255,0
visibility full

track X_track_Aorta-Endothel-Z0000043G
bigDataUrl http://www.cs.huji.ac.il/~jrosensk/gb_data_revised/Aorta-Endothel-Z0000043G.X.bigwig
shortLabel bX_data_Aorta-Endothel-Z0000043G
longLabel Other reads (mixed methylation)
parent st_UXM_Aorta-Endothel-Z0000043G on
type bigWig
viewLimits 0:1
color 255,255,0
visibility full

track M_track_Aorta-Endothel-Z0000043G
bigDataUrl http://www.cs.huji.ac.il/~jrosensk/gb_data_revised/Aorta-Endothel-Z0000043G.M.bigwig
shortLabel aM_data_Aorta-Endothel-Z0000043G
longLabel Mostly Methylated reads proportion
parent st_UXM_Aorta-Endothel-Z0000043G on
type bigWig
viewLimits 0:1
color 255,0,0
visibility full

track st_UXM_Saphenous-Vein-Endothel-Z000000RM
type bigWig
container multiWig
aggregate stacked
showSubtrackColorOnUi on
alwaysZero on
autoScale off
viewLimits 0:1
windowingFunction mean
maxHeightPixels 60:10:5
shortLabel UXM_Saphenous-Vein-Endothel-Z000000RM
longLabel UXM_stacked_Saphenous-Vein-Endothel-Z000000RM

parent st_Endothel_super
visibility full
priority 6


track U_track_Saphenous-Vein-Endothel-Z000000RM
bigDataUrl http://www.cs.huji.ac.il/~jrosensk/gb_data_revised/Saphenous-Vein-Endothel-Z000000RM.U.bigwig
shortLabel cU_data_Saphenous-Vein-Endothel-Z000000RM
longLabel Mostly Unmethylated reads proportion
parent st_UXM_Saphenous-Vein-Endothel-Z000000RM on
type bigWig
viewLimits 0:1
color 0,255,0
visibility full

track X_track_Saphenous-Vein-Endothel-Z000000RM
bigDataUrl http://www.cs.huji.ac.il/~jrosensk/gb_data_revised/Saphenous-Vein-Endothel-Z000000RM.X.bigwig
shortLabel bX_data_Saphenous-Vein-Endothel-Z000000RM
longLabel Other reads (mixed methylation)
parent st_UXM_Saphenous-Vein-Endothel-Z000000RM on
type bigWig
viewLimits 0:1
color 255,255,0
visibility full

track M_track_Saphenous-Vein-Endothel-Z000000RM
bigDataUrl http://www.cs.huji.ac.il/~jrosensk/gb_data_revised/Saphenous-Vein-Endothel-Z000000RM.M.bigwig
shortLabel aM_data_Saphenous-Vein-Endothel-Z000000RM
longLabel Mostly Methylated reads proportion
parent st_UXM_Saphenous-Vein-Endothel-Z000000RM on
type bigWig
viewLimits 0:1
color 255,0,0
visibility full

[Jonathan Rosenski]

I have tried also removing the compositeTrack and superTrack. But still the priority was not used to determine order.

Here is the updated trackDb.txt

[Gerardo Perez]

Hello, Jonathan.

Thank you for your follow-up question.

We were able to display the tracks in the assigned order from your trackDb.txt: http://genome.ucsc.edu/s/gperez2/mlq_32261_priority

One reason for not seeing the assigned priority order could be that you are encountering a caching issue where the genome browser still displays the same settings even though you updated your track hub. You can try and change the order by mouse hovering to "View" on the top blue bar menu and clicking "Default track order". If that does not work, you can then add &udcTimeout=1 parameter to the end of the URL in the address bar. More information about this URL parameter can be found on the following help page, https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Debug.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute