Inquiry Regarding Hosting FAANG Data on UCSC Genome Browser
DAILU GUAN
Dailu Guan
Assistant Project Scientist
University of California, Davis
Gerardo Perez
Hello,
Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.
Your FAANG data would be of great interest to the research community on the UCSC Genome Browser.
We took a look at your data and noticed that you have created multiple track hubs. Would it be possible to combine them into a single hub?
We also noticed that each hub contains many tracks. You might consider organizing related tracks under parent tracks using composite track structures. For example, you could group tracks into one composite for histones, one for RNA-seq, one for methylation, and one for ChromHMM annotations.
Here is the quick start guide to organizing track hubs into groupings: https://genome.ucsc.edu/goldenpath/help/hubQuickStartGroups.html
You may also find these hub examples useful: https://genome.ucsc.edu/goldenPath/help/publicHubGuidelines.html#publicHubExamples
ENCODE trackDb.txt examples:
DNA: https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/hg38/trackDb.txt
RNA-seq: https://storage.googleapis.com/gcp.wenglab.org/hubs/rna22/hg38/trackDb.txt
Integrative: https://storage.googleapis.com/gcp.wenglab.org/hubs/integrative52/hg38/trackDb.txt
We also have a tool that can help create composites and super-tracks based on your directory structure.
If you have questions or would like help getting started, we are happy to assist.
When your hub is ready, we would be glad to include it on our Public Hubs page (https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs). Submission guidelines are available here: https://genome.ucsc.edu/goldenPath/help/publicHubGuidelines.html
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
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/C62CFBC6-DD8C-458C-8858-BE173D6DED1D%40ucdavis.edu.
DAILU GUAN
Thank you again for your helpful response and thoughtful suggestions.
We will follow your guidance and begin preparing a consolidated track hub for the cattle FAANG data, organizing the tracks into composite structures by data type as recommended.
In addition, we are also working with FAANG datasets for chicken, which are aligned to the latest Ensembl genome assembly GRCg7b. We would greatly appreciate it if UCSC could consider adding support for this assembly so that we can visualize and share these data via your platform. The relevant files are available from Ensembl:
<PastedGraphic-1.png>
Hiram Clawson
Please note the search form on the 'gateway' page:
https://genome.ucsc.edu/cgi-bin/hgGateway
At the left of the page with the prompt:
"Search through thousands of genome browsers"
If you enter grcg7b in that form, you will be directed
to the assembly: GCF_016699485.2 in the browser at:
https://genome.ucsc.edu/h/GCF_016699485.2
There are NCBI RefSeq gene tracks on that browser.
--Hiram
On 5/23/25 1:29 PM, 'DAILU GUAN' via UCSC Genome Browser Public Support wrote:
> Dear Gerardo,
>
> Thank you again for your helpful response and thoughtful suggestions.
>
> We will follow your guidance and begin preparing a consolidated track hub for the cattle FAANG data, organizing the tracks into composite structures by data type as recommended.
>
> In addition, we are also working with FAANG datasets for chicken, which are aligned to the latest Ensembl genome assembly GRCg7b. We would greatly appreciate it if UCSC could consider adding support for this assembly so that we can visualize and share these data via your platform. The relevant files are available from Ensembl:
>
> FASTA: https://ftp.ensembl.org/pub/release-114/fasta/gallus_gallus/dna/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna.toplevel.fa.gz
>
> GTF annotation: https://ftp.ensembl.org/pub/release-114/gtf/gallus_gallus/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.114.gtf.gz
>
> Please let me know if adding this assembly might be feasible or if there is anything we can do to support the process.
>
> Thank you again for your continued support. I look forward to making the updated cattle track hub available to the community and exploring visualization options for the chicken data as well.
>
> Best regards,
> Dailu Guan
> Assistant Project Scientist
> Department of Animal Scientist
> University of California, Davis
>
>
>
>
>> On May 23, 2025, at 11:07, Gerardo Perez <gpe...@ucsc.edu> wrote:
>>
>> Hello,
>>
>> Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.
>>
>> Your FAANG data would be of great interest to the research community on the UCSC Genome Browser.
>>
>> We took a look at your data and noticed that you have created multiple track hubs. Would it be possible to combine them into a single hub?
>>
>> We also noticed that each hub contains many tracks. You might consider organizing related tracks under parent tracks using composite track structures. For example, you could group tracks into one composite for histones, one for RNA-seq, one for methylation, and one for ChromHMM annotations.
>>
>> Here is the quick start guide to organizing track hubs into groupings: https://genome.ucsc.edu/goldenpath/help/hubQuickStartGroups.html
>>
>> You may also find these hub examples useful: https://genome.ucsc.edu/goldenPath/help/publicHubGuidelines.html#publicHubExamples
>>
>> ENCODE trackDb.txt examples:
>>
>> DNA: https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/hg38/trackDb.txt
>>
>> RNA-seq: https://storage.googleapis.com/gcp.wenglab.org/hubs/rna22/hg38/trackDb.txt
>>
>> Integrative: https://storage.googleapis.com/gcp.wenglab.org/hubs/integrative52/hg38/trackDb.txt
>>
>> We also have a tool that can help create composites and super-tracks based on your directory structure.
>>
>> If you have questions or would like help getting started, we are happy to assist.
>>
>> When your hub is ready, we would be glad to include it on our Public Hubs page (https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs). Submission guidelines are available here: https://genome.ucsc.edu/goldenPath/help/publicHubGuidelines.html
>>
>> Gerardo Perez
>> UCSC Genomics Institute
>>
>>
>> On Thu, May 22, 2025 at 3:25 PM 'DAILU GUAN' via UCSC Genome Browser Public Support <gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>> wrote:
>>>
>>> Dear UCSC Genome Browser Team,
>>>
>>> I hope this message finds you well.
>>>
>>> My name is Dailu Guan, and I am an Assistant Project Scientist at the University of California, Davis. I am currently working with functional genomics data from the FAANG project (https://genome.ucsc.edu/s/dguan/Integrative%20BovineFAANG%20epigenomics) led by Prof. Huaijun Zhou (cced) and would like to explore the possibility of visualizing selected datasets through the UCSC Genome Browser.
>>>
>>> Specifically, we have generated high-quality regulatory annotations (e.g., ATAC-seq, ChIP-seq, RNA-seq) for livestock species (please the cattle example attached), and we believe UCSC’s platform would be an ideal resource to make a subset of these data more accessible to the entire research community for a long time. We are particularly interested in creating a track hub or collaborating to host a curated set of FAANG data tracks to support ongoing and future efforts.
>>>
>>> Would it be possible to discuss how best to proceed with this? I’d be happy to provide more details on the dataset structure, formats (e.g., bigWig, bigBed), and hosting options.
>>>
>>> Thank you very much for your time and consideration.
>>>
>>>
>>> Best regards,
>>> Dailu Guan
>>> Assistant Project Scientist
>>> University of California, Davis
>>>
>>>
>>>
>>> <PastedGraphic-1.png>
>>>
>>> --
>>>
>>> ---
>>> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
>>> To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/C62CFBC6-DD8C-458C-8858-BE173D6DED1D%40ucdavis.edu <https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/C62CFBC6-DD8C-458C-8858-BE173D6DED1D%40ucdavis.edu?utm_medium=email&utm_source=footer>.
>
Jairo Navarro Gonzalez
Hello,
I wanted to follow up with some helpful documentation about creating a track hub for a GenArk assembly.
Creating a track hub for a GenArk assembly:
https://genome.ucsc.edu/FAQ/FAQlink.html#genArkTrackHub
GenArk blog post:
https://genome-blog.soe.ucsc.edu/blog/2021/08/13/sharing-data-with-sessions-and-urls/#GenArk
Example track hub for GenArk:
https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubGenArkExample/genArkTrackHub/hub.txt
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 unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/c41d295c-a022-4f97-afa9-3fcb5eebaed9%40soe.ucsc.edu.