Baboon liftOver to hg19

[Harris, Ronald Alan]

Hi,

 

For the latest baboon assembly (papAnu2) the only liftOver file available is to papHam1. Have you already generated a hg19 liftOver file (papAnu2ToHg19.over.chain) and not put it on the site yet or do you still need to generate the liftOver file? If you still need to generate the liftOver file could you give me a rough time estimate as to when that might happen.

 

Thanks,

 

Alan

 

 

R. Alan Harris, Ph.D.

Assistant Professor

Department of Molecular and Human Genetics

Department of Obstetrics and Gynecology

Baylor College of Medicine

Houston, TX 77030

713-798-7695

[Luvina Guruvadoo]

Hello Alan,

Thank you for your question. This file has been created and is now available for download here: http://hgdownload.soe.ucsc.edu/goldenPath/papAnu2/liftOver/

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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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[Harris, Ronald Alan]

Hi,

I do not see the following liftOver files on your site:

rheMac2ToPapAnu2.over.chain.gz
papAnu2ToRheMac2.over.chain.gz

Have you already generated the files and not put them on the site or do you still need to generate the liftOver files? If you still need to generate the liftOver files could you give me a rough time estimate as to when that might happen.

[Jonathan Casper]

Hello Alan,

Thank you for your question about liftOver files between the rheMac2 and papAnu2 genome assemblies. We do not have these files prepared, but one of our engineers has offered to create them in the next couple of weeks. I will send you a follow-up message as soon as the files are ready.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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[Jonathan Casper]

Hello Alan,

The liftOver chains you requested are now available on our test download server at http://hgdownload-test.sdsc.edu/goldenPath/rheMac2/liftOver/ and http://hgdownload-test.sdsc.edu/goldenPath/papAnu2/liftOver/. The alignments underlying those chains are available at http://hgdownload-test.cse.ucsc.edu/goldenPath/rheMac2/vsPapAnu2/ and http://hgdownload-test.cse.ucsc.edu/goldenPath/papAnu2/vsRheMac2/, respectively. These files will be transferred to our main download server in the next few days.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

[Harris, Ronald Alan]

Hi,

An improved rhesus macaque assembly has recently been made public through NCBI:

http://www.ncbi.nlm.nih.gov/assembly/GCF_000772875.2

Does the UCSC group have an interest in setting up a browser for this assembly and if so should I contact someone specific regarding this?

We are particularly interested in liftOver chains between this rhesus assembly and human hg19 and hg38. Is that something your group would be interested in generating?

Let me know if you have any questions.

Thanks,

Alan

R. Alan Harris, Ph.D.
Assistant Professor
Department of Molecular and Human Genetics

[Luvina Guruvadoo]

Hello Alan,

We received a similar question from another user last week; please see our reply here:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/I6fIGAuIous/mJ4q5vBzEwAJ

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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

[Rogers, Jeffrey]

Hello Luvina,

  There is a newer upgraded assembly – subsequent to MacaM.  This improvement is now on NCBI with the designation of: Mmul_8.0.1.

It would REALLY be appreciated if your group could generate all the relevant resources you can so that the community can move to this new assembly.  As you know, rhesus are the most widely used nonhuman primate in medical research.

Thanks,

Jeff

______________________________________________

Jeffrey Rogers, Ph.D.

Associate Professor

Human Genome Sequencing Center

Dept. of Molecular and Human Genetics

Baylor College of Medicine

One Baylor Plaza

Houston, Texas  77030

email: jr...@bcm.edu

phone: 713-798-7783

[Steve Heitner]

Hello, Jeff.

As of last week, we have officially added the rheMac8 assembly to the list of assemblies we intend to add to the Browser, though we cannot provide a time estimate of when it might become available.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  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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Steve Heitner
UCSC Genome Bioinformatics Group

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[Harris, Ronald Alan]

Hi Steve,

Assemblies for the Old World monkeys listed below are now available. It would be great if UCSC included these in the browser and provided liftOver files among all the various OWM and human. Is this something you would interested in doing and if so do you have any estimate as to how long it would take?

Let me know if you have any questions or if there is any way we can help you with this.

Thanks,

Alan

Pigtail Macaque

http://www.ncbi.nlm.nih.gov/assembly/GCF_000956065.1/

Sooty Mangeby

http://www.ncbi.nlm.nih.gov/assembly/GCF_000955945.1

Drill

http://www.ncbi.nlm.nih.gov/assembly/GCF_000951045.1/

Colobus

http://www.ncbi.nlm.nih.gov/assembly/GCF_000951035.1/

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From: Steve Heitner <st...@soe.ucsc.edu>
Sent: Monday, February 1, 2016 1:49 PM
To: Rogers, Jeffrey; 'Luvina Guruvadoo'; Harris, Ronald Alan
Cc: gen...@soe.ucsc.edu
Subject: RE: [genome] New Rhesus Macaque Assembly at NCBI

 

[Cath Tyner]

Hello Alan,

The UCSC Genome Browser team is very interested in hosting these new assemblies and generating associated liftOver files, but we are unable to prioritize this work for a near-future completion date. While these assemblies could very well be added

​ in the future​

, a completion time is unknown.

You may already know about these resources:

​DIY liftOver​

Generate your own liftOver files to convert annotations

​.​

Assembly Hubs

Assembly Hubs allow researchers to create Track Data Hubs on assemblies that are not in the UCSC Browser.

Public Hub Guidelines

​Guidelines for m​

aking your assembly hub public

​ally accessible​

on the UCSC Genome Browser

​.​

Please respond to this list if you have further questions!

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

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private data help: Email

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Harris, Ronald Alan]

Hi,

An improved baboon assembly has recently been made public through NCBI:

https://www.ncbi.nlm.nih.gov/assembly/GCA_000264685.2

Does the UCSC group have plans to set up a browser for this assembly and if so should I contact someone specific regarding this?

We are particularly interested in liftOver chains between the new baboon assembly and papAnu2 as well as hg38. Is that something your group is planning on generating? 

Let me know if you have any questions.

Thanks,

Alan

R. Alan Harris, Ph.D.
Assistant Professor

Human Genome Sequencing Center

[Jairo Navarro Gonzalez]

Dear Alan,

Thank you for your question about the release of the new baboon assembly. Unfortunately, we do not have a specific release date at this time, and we will post an announcement as soon as the assembly becomes available.

If you would like email updates about the UCSC Genome Browser, you can subscribe to our Announcements List:

• Subscribe: Email genome-annou...@soe.ucsc.edu
• Unsubscribe: Email genome-announ...@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 Genomics Institute

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[Harris, Ronald Alan]

Hi,

An improved rhesus macaque assembly has recently been made public through NCBI:

https://www.ncbi.nlm.nih.gov/assembly/GCF_003339765.1

Does the UCSC group have plans to set up a browser for this assembly and if so should I contact someone specific regarding this?

We are particularly interested in liftOver chains between the new rhesus assembly and hg19/hg38. Is that something your group is planning on generating and if so, when?  

[Luis Nassar]

Hello Alan,

Thank you for your interest in the Genome Browser.

We are currently processing this new assembly (rheMac10). I cannot offer an exact timeline for when we would release the assembly to our live site, but the supporting liftOver files should be available earlier. Likely in the next week or two.

Lou Nassar
UCSC Genomics Institute

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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[Luis Nassar]

Hello Alan,

The liftOver files can now be found in the our downloads directory.

rheMac10: http://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/liftOver/

There are also liftOver files available to/from hg19, hg38, rheMac8, and mm10. You will find those in the respective database liftOver folder.

Lou Nassar

UCSC Genomics Institute

[Harris, Ronald Alan]

Hi,

A new cynomologous macaque (crab-eating macaque) long read assembly has recently been made public through NCBI:

https://www.ncbi.nlm.nih.gov/assembly/GCA_011100615.1

Does the UCSC group have plans to set up a browser for this assembly and if so should I contact someone specific regarding this?

We are particularly interested in liftOver chains between the new cynomologous assembly and hg19/hg38. Is that something your group is planning on generating and if so, when?  

[Matthew Speir]

Hello, Alan. 

Thank you for letting us know about the release of this new crab-eating macaque assembly at NCBI. We have made a note of it in our internal work queue, although I can't give an estimate of when it will be available on our site.

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.

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

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

---

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.

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