chain file for hg38 to hs1 liftover

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Robert Linder

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Mar 5, 2024, 7:53:21 PMMar 5
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Hi,

I was wondering if there is a chain file available for lifting over hg38 to the T2T hs1? I can find a chain file for going from hs1 to hg38, but I can't find one going the other way. My file is >1GB, so it'd be great if I could use the standalone version of liftover. Thanks!!

Best,
Rob

Jairo Navarro Gonzalez

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Mar 5, 2024, 8:01:37 PMMar 5
to Robert Linder, gen...@soe.ucsc.edu

Hello,

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

We recently had an issue with the download server that resulted in some missing files. We have restored the liftOver file for hg38:

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToGCA_009914755.4.over.chain.gz

Thank you again for bringing this to our attention.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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Jairo Navarro
UCSC Genome Browser


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Robert Linder

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Apr 4, 2024, 12:13:59 PMApr 4
to Jairo Navarro Gonzalez, gen...@soe.ucsc.edu
Hi Jairo,

Sorry to bug you again, but I'm trying to make a chain file using mm39 as the target genome and balb_cJ_v3 ( https://www.ebi.ac.uk/ena/browser/view/GCA_921997145.2) 
as the query genome. However, I'm getting an error when running the liftOver perl script that I cannot seem to resolve. Would it be possible for someone on your team to generate the chain file for these assemblies? Thanks so much!

Best,
Rob
From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: Tuesday, March 5, 2024 5:01 PM
To: Robert Linder <rli...@sbpdiscovery.org>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] chain file for hg38 to hs1 liftover
 
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Gerardo Perez

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Apr 4, 2024, 8:53:10 PMApr 4
to Robert Linder, gen...@soe.ucsc.edu
Hello, Rob.

Thank you for your interest in the Genome Browser.

The mm39 to GCA_921997145.2 BALB_cJ_v3 chain file is available on our downloads server:

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

Robert Linder

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Apr 5, 2024, 12:42:02 PMApr 5
to Gerardo Perez, gen...@soe.ucsc.edu
Hi Gerardo,

This is perfect- thanks so much! Have a great weekend!

Best,
Rob
From: Gerardo Perez <gpe...@ucsc.edu>
Sent: Thursday, April 4, 2024 5:52 PM

To: Robert Linder <rli...@sbpdiscovery.org>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] chain file for hg38 to hs1 liftover
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Robert Linder

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Jun 4, 2024, 6:46:16 PMJun 4
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Hi,

If possible, could a lift-over chain file be generated with mm39 as the target genome and C57BL_6NJ_v3 (https://www.ebi.ac.uk/ena/browser/view/GCA_921999865.2) as the query genome? Thanks so much!
Best,
Rob


From: Gerardo Perez <gpe...@ucsc.edu>
Sent: Thursday, April 4, 2024 5:52 PM

To: Robert Linder <rli...@sbpdiscovery.org>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] chain file for hg38 to hs1 liftover
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Matthew Speir

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Jun 24, 2024, 11:32:05 AM (9 days ago) Jun 24
to Robert Linder, gen...@soe.ucsc.edu
Hello, Rob.

I apologize for the delay in getting back to you. We should have the LiftOver file between mm39 and GCA_921999865.2 available shortly.

Thank you for your patience.
---

Matthew Speir

UCSC Genome Browser, User Support


Matthew Speir

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Jun 26, 2024, 12:29:09 PM (6 days ago) Jun 26
to Robert Linder, gen...@soe.ucsc.edu
Hello, Rob.

These files are now available on our downloads server:
And there is now a GenArk hub available for C57BL_6NJ_v3: https://genome.ucsc.edu/h/GCA_921999865.2


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

Robert Linder

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Jun 26, 2024, 3:00:53 PM (6 days ago) Jun 26
to Matthew Speir, gen...@soe.ucsc.edu
Hi Matthew,

That's perfect -thanks so much!!

Best,
Rob
From: Matthew Speir <msp...@ucsc.edu>
Sent: Wednesday, June 26, 2024 9:28 AM
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