No mouseOver effect in my track hub on UCSC genome browser

Question

[Pei]

Hello!

I generated a track hub to share my ChIP read coverage with my collaborator through UCSC genome browser. The tracks are in bigWig format and when each track was submited individually, mouse-over works as expected (That means, one could move the mouse over a genomic locus and the corresponding read coverage will be displayed).

However, when I combined multiple tracks into a track group (container multiWig), the mouseover effect was gone, so nothing will be displayed even I move the mouse over a peak.

Are there any parameter I missing?

Please feel free to let me know if anything I need to do.

Thank you!

Pei

Answer 1

[Pei]

After review my hub file, some nice guys from UCSC Genome Browser team suggested me to

"convert you file to another container type, notably a composite (https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#compositeTrack). You will lose a few functionalities such as overlaying/merging the tracks, but otherwise, it is very similar. To convert your file you only have to replace "container multiWig" with "compositeTrack on". The following sed command works for this task:

sed -i "s/container multiWig/compositeTrack on/g" display\?to_ext\=txt. "

Answer 2

[Pei]

More feedback from one nice guy at the UCSC genome browser team.

if you are looking to use the overlay feature collections are a great idea. They are somewhat like modified multiwigs under the hood, but the mouseovers are working when the merge method is set to "none", "add", or "subtract". We don't show a mouseover when they are overlayed since it isn't clear exactly what value you would display in those scenarios.

Track collections expire after a few days, however, if you save them to a session (https://genome.ucsc.edu/cgi-bin/hgSession) then they stick around permanently. So the best way to share data with collaborators as you describe would be to create track collections and share session links.

You can create multiple collections in a single browser view, essentially replicating how you have your hub (or any other combination). Then save that in a single session to have all the data under one URL.

You can edit the height of the Y-axis in the collection track description page "track height". To change the limits of what Y-axis you can change the vertical viewing range and data scaling options.