New zebrafish assembly

[Pol Sorigué Tomàs]

Hi,

I will soon start a project on zebrafish methylation patterns. I noticed that there is a very recent new assembly of zebrafish (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_049306965.1/).

Currently, the information in the UCSC Genome Browser on CpG islands in zebrafish is based on the previous assembly, and I was wondering if you foresee an update on CpG island information for the new assembly

Best,

Pol Sorigué

 

[Maximilian Haeussler]

Hi Pol,

a brand new assembly will have almost no annotation data. If you are looking for actual methylation data, did you see the Danio Code track hub? You can connect to it in the menu via My Data > Track Hubs. More info here: https://danio-code.zfin.org/

best

Max

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[Matthew Speir]

Hello, Pol.

As my colleague Max shared, if you're interested in methylation data, a brand-new assembly is unlikely to have any significant annotations.

However, if you're interested in just the pre-computed CpG islands track, we can import the new assembly and generate that for you.

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.

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[Pol Sorigué Tomàs]

Hi Matthew,

Thank you so much for your response.

Given that I'm not expert at all, I think I would very much appreciate if it would be possible to have access to such pre-computed CpG island track. Only, of course, if this is not a burden for you.

The clock is ticking for my PhD and this would be very helpful for my purpose.

Thank you in advance.

All the best,

Pol Sorigué

 

If this email reaches your inbox outside of your usual working hours, please note I do not expect that you will respond to, or act on it.

 

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De: Matthew Speir <msp...@ucsc.edu>
Enviado: viernes, 30 de mayo de 2025 21:21
Para: Maximilian Haeussler <mhae...@ucsc.edu>
Cc: Pol Sorigué Tomàs <pol....@gimm.pt>; gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Asunto: Re: [genome] New zebrafish assembly

 

No suele recibir correo electrónico de msp...@ucsc.edu. Por qué es esto importante

[Luis Nassar]

Hi, Pol.

We're working on importing this assembly. The process typically takes about a week, but can vary depending on our current bandwidth. We'll let you know when it's ready.

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/AM9SPR01MB00227BE0FE06F5821E9F6FE7E760A%40AM9SPR01MB0022.eurprd07.prod.outlook.com.

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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

[Pol Sorigué Tomàs]

Thank you so much! 

I look forward to hearing from you again.

All the best,

Pol Sorigué

 

If this email reaches your inbox outside of your usual working hours, please note I do not expect that you will respond to, or act on it.

 

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De: Luis Nassar <lrna...@ucsc.edu>
Enviado: jueves, 5 de junio de 2025 0:09
Para: Pol Sorigué Tomàs <pol....@gimm.pt>
Cc: Matthew Speir <msp...@ucsc.edu>; Maximilian Haeussler <mhae...@ucsc.edu>; gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>

Asunto: Re: [genome] New zebrafish assembly

 

No suele recibir correo electrónico de lrna...@ucsc.edu. Por qué es esto importante

[Luis Nassar]

Hi, Pol.

This genome browser is now available here: https://genome.ucsc.edu/h/GCF_049306965.1

You will also find the two CpG island files on our download server: https://hgdownload.soe.ucsc.edu/hubs/GCF/049/306/965/GCF_049306965.1/bbi/

Let us know if you have any additional items we can help with.

[Luis Nassar]

Hi, Pol. 

The assembly URL I shared will be active tomorrow. In the meantime, you can access the assembly here: https://genome.ucsc.edu/cgi-bin/hgTracks?genome=GCF_049306965.1&hubUrl=/gbdb/genark/GCF/049/306/965/GCF_049306965.1/hub.txt

[Pol Sorigué Tomàs]

Thank you so much for letting me know, and for doing all this!

It will be very helpful for me

All the best,

Pol Sorigué

 

If this email reaches your inbox outside of your usual working hours, please note I do not expect that you will respond to, or act on it.

 

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De: Luis Nassar <lrna...@ucsc.edu>
Enviado: martes, 10 de junio de 2025 15:32