Fw: [genome-www] Re: Next update of JASPAR tracks for the UCSC genome browser
Rafael Riudavets Puig
Sent: 20 July 2023 18:35
To: Rafael Riudavets Puig
Cc: Anthony Mathelier; Ieva Rauluseviciute
Subject: Re: [genome-www] Re: Next update of JASPAR tracks for the UCSC genome browser
Jairo Navarro
UCSC Genome Browser
UC Santa Cruz Genomics Institute
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Dear Jairo,
For the track hubs, would we need to recompute all the tracks for previous JASPAR releases? If that was the case, we would really like to avoid doing this, since these tracks can be quite heavy and we would prefer to compute only what is needed. Additionally, I think that the pages containing more details for a TFBS (see here for an example) were computed internally at UCSC, since I could not find the code generating them anywhere.
I also wanted to bring to your attention that the current native tracks for the 2022 release seem to be outdated. For example, this TFBS is annotated as TFAP4::ETV1, with matrix ID MA1779.1. However, this matrix ID in JASPAR corresponds to a completely different profile. The last update of the UCSC tracks seems to have happened on 2021-12-23, but our latest version of the tracks dates to 2022-05-07 (you can find the bigBed files here). My best guess is that there was a miscommunication when the tracks got updated on our side and this update did not happen on the UCSC side. In any case, since the current native tracks will need to be updated and we will soon publish a new JASPAR release, I would suggest that we find a specific and standard workflow to update/fix the genome browser tracks when needed. Ideally, we would prefer if it was possible to do so from a set of files or a trackHub that we make available at some URL, while not having to unnecessarily recompute tracks for previous releases.
If you want, we could schedule a videocall to more easily discuss this in person.
Best regards,
Rafael Riudavets Puig
From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: 04 July 2023 23:42:57
To: Rafael Riudavets Puig
Cc: Anthony Mathelier; genome-www
Subject: Re: [genome-www] Re: Next update of JASPAR tracks for the UCSC genome browserHello,
Thank you for using the UCSC Genome Browser and sending your hub.
For the next step, you can update the current JASPAR hub with all the new 2024 data files and settings, similar to previous years:
This way, the data can be publicly available for users while we work on updating the native JASPAR track. Once the data is available on the JASPAR hub, let us know, and we can update the track on the UCSC Genome Browser.
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 Tue, Jul 4, 2023 at 8:50 AM Rafael Riudavets Puig <r.r....@ncmm.uio.no> wrote:
Dear Jairo,
Thank you very much for the information.
The tracks follow the same methodology, so the only difference will be that the new bigBed files will contain more intervals and the text in the info HTML page will also be updated with things like citations.
I created a mock lighter hub with a couple of assemblies just so that you can see how things will look. You can find it here: https://frigg.uio.no/ftp/mathelier/JASPAR_genome_browser_tracks/2024/hub.txt.
Please note that in the current native tracks, the interval-specific pages contain information such as a visualization of the position frequency matrices (e.g. https://genome-euro.ucsc.edu/cgi-bin/hgc?hgsid=299098668_KNuL4pmOkytznNxKaEaXlRVz3gw3&db=hg38&c=chr2&l=25160914&r=25168903&o=25161337&t=25161348&g=jaspar2022&i=MA0060.3). As far as I know, these visualization were produced on the UCSC side.
What do you think would be the best course of action?
Best regards,
Rafael Riudavets Puig
From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: 30 June 2023 01:29:08
To: Rafael Riudavets Puig; Anthony Mathelier
Cc: genome-www
Subject: Re: [genome-www] Re: Next update of JASPAR tracks for the UCSC genome browserHello,
Thank you for using UCSC Genome Browser and sending your inquiry.
We are interested in updating the native JASPAR tracks with the most recent data. Is there a significant difference in the methodology of this release compared to the previous version, or does this new release use the same pipeline as before?
For now, it would be best to create a hub for the new JASPAR update to review the data and ensure that no necessary files are missing when updating the native tracks. You can find the public hub guidelines on the following wiki page:
http://genome.ucsc.edu/goldenPath/help/publicHubGuidelines.html
After the hub is created, please send us the URL to the hub.txt file so we can review the hub and proceed to the next steps.
I hope this is helpful. If you have any further questions, please reply to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
On Mon, Jun 26, 2023 at 3:23 PM 'Daniel Schmelter' via UCSC Genome Browser Confidential Support <genom...@soe.ucsc.edu> wrote:
Hello Rafael,
Thank you for your message. Unfortunately, I am no longer a part of the UCSC Genome Browser team and so I cannot advise you on their current needs. Generally, I can tell you that native tracks only require bigBeds and the internal team handles the settings that would be in a trackDb.txt and the HTML page, though they may be open to collaboration.
I have CC'd the Genome-www email where current Browser staff can help you.
Wishing you all the best,Daniel
--On Mon, Jun 19, 2023 at 1:12 AM Rafael Riudavets Puig <r.r....@ncmm.uio.no> wrote:
Dear Daniel Schmelter,
My name is Rafael Riudavets Puig, I am working with the JASPAR team at Anthony Mathelier's lab.
We are currently on the process of preparing all the data for our next release. Since the JASPAR TFBS tracks are now part of the browser's native tracks, we would like to make sure that we are providing all files that would be needed for the update on your side. I discussed with Oriol Fornes, the person who previously prepared all the data, and he told me I would just need to prepare the bigBed files and make them available somewhere for you to download. However, I would like to ask just to make sure: is there anything else you would need in order to do the update? For example, would you need files such as the hub.txt, genomes.txt, trackDb.txt, HTMLs, etc that are usually needed to build a trackHub?
Looking forward to hearing from you,
Rafael Riudavets Puig
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Jairo Navarro Gonzalez
Hello,
I apologize for the confusion in my last email, we are not requesting that you update the previous versions of JASPAR in your track hub. Instead, we request that you create a final version of the mock hub you shared in a previous email:
https://frigg.uio.no/ftp/mathelier/JASPAR_genome_browser_tracks/2024/hub.txt
Once the 2024 hub meets the public hub guidelines, we can begin to update the native track on the UCSC Genome Browser.
http://genome.ucsc.edu/goldenPath/help/publicHubGuidelines.html
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
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