How to make track collections of stranded data such as RNA-seq (from a track hub) to display properly

[Gamliel, Amir]

Hello,

I am trying to make a track collection of stranded PRO-seq data (similar to RNA-seq). The data is in a track hub, and shows up correctly. However, if I try to make a track collection from multiple track hubs, (i.e. so that I can compare levels between samples using group auto-scale), the track collection separates each strand to a distinct row, and does not “stack” them properly. See example below.

Perhaps this is a trivial setting, but I could not find how to do it in any of the documentation.

Thanks so much,

Amir

PS.  You can also see my attempts in this link:

Here is a UCSC browser session I'd like to share with you: http://genome.ucsc.edu/s/agamliel/Pro%2Dseq_MCF7_16HD_E2_timecourse_180608

Amir Gamliel, PhD
Dept. of Medicine
University of California, San Diego
9500 Gilman Drive, Mail Code 0648
La Jolla, California 92037-0648
phone: 858-534-7294
fax: 858-534-8180
e-mail: agam...@ucsd.edu

[Jairo Navarro Gonzalez]

Hello,

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

To use a merge method for the track collection, you will have to enable the setting on the track configuration page. You can access this page by clicking on the collection name underneath the browser image, or right-clicking the track collection and selecting the "Configure Pro-seq track set". Once on the configuration page, you can set the merge method to "stacked" or any of the other overlay methods. Here is a session with your track collections set to the "stacked" merge method, http://genome.ucsc.edu/s/jnavarr5/hg19.MLQ_28718.

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

Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining

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[Gamliel, Amir]

Hello Jairo,

Thank you so much for your quick response! I think I may have misused the term “stacked” as that was not what I was intending. Indeed, when comparing multiple tracks in a collection, stacking them condenses the view to allow comparison between different condition. However, if you have too many tracks, as in my example below, stacking them actually obscures the patterns occurring between samples. That’s why I love using collections for ChIP-seq data , with no merging (or stacking), as it allows to set all the tracks within the collection the same Y axis settings (via “group auto-scale”). That works great for track with just positive values. However, for RNA-seq or PRO-seq tracks that have data both positive and negative, it changes the appearance or the “packing” of the plus strand on top of the minus strand. To give an example, see the image below, how currently the collection separates the minus and plus strand, and how I would like it to look. The way I did that was just to use the original tracks (not their collection) and manually configure the vertical viewing range of each track to be identical. This of course becomes very  tedious  since each genomic location will have different tag density. That’s why it would be useful to do in the collection.

I hope I made myself more clear, 

Thank again for all your help,

Best,

Amir

Amir Gamliel, PhD
Dept. of Medicine
University of California, San Diego
9500 Gilman Drive, Mail Code 0648
La Jolla, California 92037-0648
phone: 858-534-7294
fax: 858-534-8180
e-mail: agam...@ucsd.edu

On Jan 6, 2022, at 3:38 PM, Jairo Navarro Gonzalez <jnav...@ucsc.edu> wrote:

Hello,

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

To use a merge method for the track collection, you will have to enable the setting on the track configuration page. You can access this page by clicking on the collection name underneath the browser image, or right-clicking the track collection and selecting the "Configure Pro-seq track set". Once on the configuration page, you can set the merge method to "stacked" or any of the other overlay methods. Here is a session with your track collections set to the "stacked" merge method, http://genome.ucsc.edu/s/jnavarr5/hg19.MLQ_28718.

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

Want to share the Browser with colleagues?
Host a workshop: https://bit.ly/ucscTraining

On Wed, Jan 5, 2022 at 1:59 PM Gamliel, Amir <agam...@health.ucsd.edu> wrote:

Hello,

I am trying to make a track collection of stranded PRO-seq data (similar to RNA-seq). The data is in a track hub, and shows up correctly. However, if I try to make a track collection from multiple track hubs, (i.e. so that I can compare levels between samples using group auto-scale), the track collection separates each strand to a distinct row, and does not “stack” them properly. See example below.

Perhaps this is a trivial setting, but I could not find how to do it in any of the documentation.

Thanks so much,

Amir

PS.  You can also see my attempts in this link:

Here is a UCSC browser session I'd like to share with you: http://genome.ucsc.edu/s/agamliel/Pro%2Dseq_MCF7_16HD_E2_timecourse_180608

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Amir Gamliel, PhD
Dept. of Medicine
University of California, San Diego
9500 Gilman Drive, Mail Code 0648
La Jolla, California 92037-0648
phone: 858-534-7294
fax: 858-534-8180
e-mail: agam...@ucsd.edu

[Matthew Speir]

Hello, Amir.

Thank you for providing those extra details as well as the labeled image indicating what you're looking for. They were very helpful.

At this time, it's not possible to have a collection with tracks organized in such a way. Having the +/- strand tracks overlaid in the way you show requires them to be in a multiWig, which is not allowed to be nested under a composite track, which is how these track collections are stored under the hood. However, we agree that it would be a useful way of organizing the data and something that has been requested by other users in the past. We've made a note of your request, which helps us prioritize our work, though I can't offer an estimate of when this feature would be available.

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.

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues? Host a workshop: http://bit.ly/ucscTraining

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/8C2B8776-1420-427B-8115-E026BA2CEAA9%40health.ucsd.edu.