Re: [genome-www] hgUserSuggestion gbenegas@berkeley.edu 2023-01-11 11:56:05

[Gonzalo Benegas]

Dear Jairo Navarro,

Thank you for your prompt response and pointing me to dynseq tracks. Unfortunately, I don't think this would work for me as I'd like to display the 4 nucleotides stacked on top of each other.

Best regards,
Gonzalo Benegas

On 1/14/23 19:27, Jairo Navarro Gonzalez wrote:

Hello,

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

The UCSC Genome Browser can display a Motif Logo that you can view on the browser. You can find an example of the Motif Logo on the following page:

https://genome.ucsc.edu/goldenpath/help/bigWig.html#Ex4

For your bigWig track, you can add the following trackDb setting, logo=on, and it will display the sequence motif.

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

On Wed, Jan 11, 2023 at 11:57 AM <genom...@soe.ucsc.edu> wrote:

SuggestionID:: gben...@berkeley.edu 2023-01-11 11:56:05
UserName:: Gonzalo Benegas
UserEmail:: gben...@berkeley.edu
Category:: Tracks
Summary:: Genome-wide sequence logo track


Details::
Hello,

Thank you for the genome browser, I use it every single day. I would appreciate a sequence logo representation of a position weight matrix available for each base of the genome. Some use cases I consider:
- Displaying constraint inferred from multiz alignments.
- Displaying constraint inferred from DNA language models, as in Fig. 3 from our recent paper [1].

Best,
Gonzalo Benegas
PhD Student - UC Berkeley

[1] Benegas, Gonzalo, Sanjit Singh Batra, and Yun S. Song. "DNA language models are powerful zero-shot predictors of non-coding variant effects." bioRxiv (2022).

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[Luis Nassar]

Hello, Gonzalo.

I believe you may be able to display the data that way.

The dynseq display my colleague shared can be combined with a special track type we have "multiWig" which is a container for bigWig tracks, and allows for some combined manipulation/display of the data.

Here, for example, is a track displaying conservation data on our development server with stacking logos the way you describe: http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=lou&hgS_otherUserSessionName=RM30472

Keep in mind that data/features on our development server have not undergone our QA process and are subject to change at any time.

If you would like to build a similar track, you can find additional information on multiWigs on our docs:

https://www.genome.ucsc.edu/goldenPath/help/hubQuickStartGroups.html#multiWig
https://www.genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#multiWig

Also, here is the trackDb entry for that track on our development server, which may help you create your own as a working example:

https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/hg/makeDb/trackDb/human/hg38/multiz100Logo.ra

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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[Gonzalo Benegas]

Dear Lou,

Thank you, that looks great! I'll give it a try.

Best,
Gonzalo

[Gonzalo Benegas]

Dear Lou,

I got it to work with my data, it looks very nice!

One question, is it possible to change the color of each nucleotide? When I modify the "color" attribute of the bigWig, it only seems to change the color on the aggregate signal (when zooming out).

Thank you!
Gonzalo

[Luis Nassar]

Hi, Gonzalo.

Thanks for pointing this out.

We have fixed this behavior so that now the logo color will be the one designated by the bigWig track (if any). This change will hit our live site during our next version release next Tuesday March 21st, so if you already have the color setting in your files you should see them change color after that date.

Let us know if you have any other questions, or notice any other strange behavior.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

[Gonzalo Benegas]

Hi Lou,
Working for me now, thank you so much!
Best,
Gonzalo

[Gonzalo Benegas]

Dear Lou,

Another question, when doing reverse complement the colors assigned to each nucleotide change as well. Would it be possible to control this? Thank you!

Best,
Gonzalo

[Gerardo Perez]

Hello, Gonzalo.

Thank you for your follow-up question.

It appears that you have found a bug in the dynseq reverse complement display. We have created an internal ticket to fix the issue. Unfortunately, we cannot provide an estimated release date for the fix but will follow up with you when the fix is in place.

Thank you again for bringing this to our attention.

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 on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/33a3dc00-adac-0592-262d-6ed4192c322f%40berkeley.edu.

[Gonzalo Benegas]

Dear Gerardo,

Thank you for supporting UCSC Genome Browser and the logo track. I've recently come across a different issue where the characters sometimes overlay on top of each other, usually upside down. Here's an example where all 4 bigwig values are positive and which was working fine a few months ago:
https://genome.ucsc.edu/s/gbenegas/gpn-arabidopsis-bug

Thank you in advance for your help.

Best,
Gonzalo

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and reporting your issues.

You have indeed discovered a bug with the sequence logo display, which has been fixed on our development server. The fix will be released to the public during the next software update on August 15th. In the meantime, you can view the fix on the preview server:

https://genome-preview.soe.ucsc.edu/

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/bf4d650c-841e-0850-ee92-7754b6e70842%40berkeley.edu.

[Gonzalo Benegas]

Dear Jairo,

Thank you for the prompt reply and information about the update, which is really appreciated.

Best,
Gonzalo