Genome browser - changing track height/scaling

[Seungho Lee]

Hello,

In the genome browser, is there a way to set the track height and scale for all tracks at once, as opposed to having to configure each track one by one? The "group auto-scale" function is also not available for some reason.

Thank you

[Brian Lee]

Dear Seungho,

Thank you for using the UCSC Genome Browser and your question about how to set the track height and scale for many tracks at once.

We do have a tool called the Track Collection Builder that allows you to accomplish this goal: http://genome.ucsc.edu/cgi-bin/hgCollection

While it only works on signal tracks, it allows you to name a collection and then move any tracks into it, and then configure them all at the same moment. To make it easier to do, you can have all the tracks visible first and then use the + icon to add them to the collection you have named.  On the above page you can click the "Quick video demo" to see how two visible tracks are put into a new Track Collection.  And then lower in the "Getting Started" section you will see step by step instructions.

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please send new questions to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum to help others find answers to similar questions. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu, which is a private internal list to our support team.

All the best,

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[Seungho Lee]

Hello,

Thank you - that was exactly what I was looking for.

 I also wanted to ask if there's a way to display tracks side by side, like below. Currently I'm taking screenshots and pasting them into powerpoint to compare the ATAC and RNA seq data at each timepoint, but does the Genome Browser have a way to display tracks this way? 

Thank you 

[Jairo Navarro Gonzalez]

Hello,

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

The Genome Browser has a multi-region mode that will allow you to view two or more genomic regions on a virtual chromosome. You can learn more about this feature from the following help page and YouTube tutorial:

https://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html
https://www.youtube.com/watch?v=ht4sGj1Tlxw&list=UUQnUJepyNOw0p8s2otX4RYQ

For example, if you wanted to view regions of chr21 and chr22 side-by-side, you would first click on the "multi-region" button and then insert the BED coordinates for the regions:

chr22 15690026 17558149 
chr21 15730025 18267373

Unfortunately, it isn't possible to display different track sets side-by-side using multi-region mode. You will have to continue to use the photo editor to get the display you want in your PowerPoint presentations.

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.

Jairo Navarro

UCSC Genome Browser

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAALjmKH-EH0E-annbNXJvPdRdd0_KNvRyUobc%3DursCxPW%2BadtQ%40mail.gmail.com.

[Hiram Clawson]

Or, you could set up two separate web browser windows on the
genome and set those two windows side by side on your desktop.

>>>> <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAALjmKHTHVd88qY5HRZYep2JohqzUTT0nF9n0hGiKvToMaWffg%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>> .

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[Bruno Wimmer]

Hey, one question, how did you now manage to adjust the scales in UCSC Genome Browser?? I dont get how the Collection Tool actually helps with that?

YOur screenshot shows how the scale is now the same everywhere. How did you manage that?

[Gerardo Perez]

Hello,

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

To adjust the scale of data for graph-based tracks, you can use the Data view scaling option available on the track's description page. For more information, please visit our Configuring Graph-Based Tracks Help Page: https://genome.ucsc.edu/goldenPath/help/hgWiggleTrackHelp.html.

If you’re working with multiple graph-based tracks, the Track Collection Builder tool might be helpful. This tool allows you to group several graph-based tracks into a composite track. By configuring the settings for the composite, those settings will automatically apply to all the tracks within the group. For instance, you can set the Data view scaling option to “group auto-scale,” which ensures that all tracks are scaled relative to the track with the highest data points in the group. For more information, please review the Track Collection Builder Help Page: https://genome.ucsc.edu/cgi-bin/hgCollection#Intro.

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

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/376b50b6-3967-4812-8a01-fe001764f2d5n%40soe.ucsc.edu.