liftover tool between primates

[Michelle Ysrael]

Hello,

I was wondering if it would be possible to create a liftover chain file to convert marmoset (callithrix jacchus) genomic coordinates to a related primate species, the cotton top tamarin? We have used liftover for domestic cat to cheetah conversions and they have worked well, so wanted to see if this was also possible.

Thank you!
Michelle Ysrael 

[Matthew Speir]

Hello, Michelle. 

Thank you for your request for LiftOver files.

Could you please provide the NCBI accession (e.g. GCA... or GCF...) or the UCSC assembly name (e.g. calJac2) for each assembly? We want to be sure we're producing a LiftOver file between the correct assemblies for you.

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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Matthew Speir

UCSC Genome Browser, User Support

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[Michelle Ysrael]

Hello,

For cotton top tamarin: GCA_031835075.1

For marmoset: GCA_011100555.2

Thank you!

Michelle Ysrael

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From: Matthew Speir <msp...@ucsc.edu>
Sent: Wednesday, July 31, 2024 4:28 PM
To: Michelle Ysrael <mys...@sdzwa.org>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] liftover tool between primates

 

[Michelle Ysrael]

Actually while we are at it, would it be possible to make a chain file for marmoset to a couple more tamarin species?

Golden lion tamarin: GCA_028533165.1

Emperor tamarin: GCA_004024885.1

I didn't realize they all had reference genomes! Thank you for your help, Michelle Ysrael

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From: Michelle Ysrael <mys...@sdzwa.org>
Sent: Thursday, August 1, 2024 9:32 AM
To: Matthew Speir <msp...@ucsc.edu>

[Matthew Speir]

Hello, Michelle.

Some of these data are now available on our downloads server:

• Marmoset (GCA_011100555.2) and Cotton-top tamarin (GCA_031835075.1)
• GCA_011100555.2 to GCA_031835075.1
• GCA_031835075.1 to GCA_011100555.2
• Marmoset (GCA_011100555.2) and Emperor tamarin (GCA_004024885.1)
• GCA_011100555.2 to GCA_004024885.1
• GCA_004024885.1 to GCA_011100555.2

These data can also be visualized as tracks on their respective genome browsers using the "Chain/Net" track under the "Comparative Genomics" group:

• https://genome.ucsc.edu/h/GCA_011100555.2
• https://genome.ucsc.edu/h/GCA_031835075.1
• https://genome.ucsc.edu/h/GCA_004024885.1 (the track isn't available just yet, but should be there in the future)

For the golden lion tamarin, the hub is available at https://genome.ucsc.edu/h/GCA_028533165.1. However, we're still working on the pairwise alignment with marmoset. It should be finished in a few days and I'll send you an email with links to the LiftOver files when they're available. 

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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Matthew Speir

UCSC Genome Browser, User Support

[Matthew Speir]

Hello, Michelle.

I apologize for the delay. These files are now available on our download server:

• GCA_011100555.2ToGCA_028533165.1
• GCA_028533165.1ToGCA_011100555.2

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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Matthew Speir

UCSC Genome Browser, User Support

[Michelle Ysrael]

Thank you so much for this! 

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From: Matthew Speir <msp...@ucsc.edu>
Sent: Wednesday, August 21, 2024 1:29 PM

[Michelle Ysrael]

Hello,

Thank you for your help with this. We need one additional liftover chain file between marmoset assemblies:

GCA_002754865.1 to GCA_011100555.2

Thank you again!
Michelle Ysrael 

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From: Matthew Speir <msp...@ucsc.edu>
Sent: Friday, August 9, 2024 8:04 AM

[Gerardo Perez]

Hello Michelle,

We apologize for the delay in our response.

We are still working on generating the chain file for GCA_002754865.1_ASM275486v1 to GCA_011100555.2_mCalJa1.2.pat.X. We've encountered some challenges with this alignment that require special attention. We’ll follow up with you as soon as we have an update.

If you have any other questions in the meantime, please don’t hesitate to reach out to us at 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/BN8PR03MB491518992B882D5E221F1E54A8712%40BN8PR03MB4915.namprd03.prod.outlook.com.

[Gerardo Perez]

Hello, Michelle.

We wanted to follow up and let you know that we have generated the GCA_002754865.1_ASM275486v1 to GCA_011100555.2_mCalJa1.2.pat.X liftOver chain file:

GCA_002754865.1 -> GCA_011100555.2:
https://hgdownload.soe.ucsc.edu/hubs/GCA/002/754/865/GCA_002754865.1/liftOver/GCA_002754865.1ToGCA_011100555.2.over.chain.gz

GCA_011100555.2 -> GCA_002754865.1:
https://hgdownload.soe.ucsc.edu/hubs/GCA/011/100/555/GCA_011100555.2/liftOver/GCA_011100555.2ToGCA_002754865.1.over.chain.gz

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