LiftOver for Chr15

[Jing Zhang]

Dear Sir/Madam,

 

I try to us LiftOver to convert genome from human GRCh37/hg19, chr15:22,572,276-23,506,059 to GRCh38/hg38, the results show : chr15:22770568-22770734, but it seems not right. Could you help to convert this location from GRCh37/hg19 to GRCh38/hg38? Thanks.

 

Best,

 

Jing

 

Jing Zhang, Ph.D.

 

Principal Scientist

Garuda Therapeutics, Inc.

215 First St, Suites 340-350

Cambridge, MA 02142

M: 617-519 3788

E: jing....@garudatx.com

https://garudatx.com

 

 

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[Matthew Speir]

Hello, Jing.

Thank you for your question about lifting coordinates between two assemblies.

There are two ways you can do this using our website:

(a) Using our "Convert" tool:
1. Go your hg19 region (chr15:22,572,276-23,506,059) in the main genome browser track image
2. Go to "View > In Other Genomes (Convert)" in the blue bar menu at the top of the page
3. Select hg38 as your "new" genome
4. Click submit.
5. You should see three results (here the second hit seems to be the best combination of similarity in terms of bases and span):

chr15:22284325-23174491 (13.0% of bases, 94.2% of span)
chr15:22367037-23226874 (81.5% of bases, 92.1% of span)
chr15:22770568-22770734 (0.0% of bases, 0.0% of span)

(b) Using our web-based LiftOver interface:
1. Go to https://genome.ucsc.edu/cgi-bin/hgLiftOver
2. Select hg19 as your "old" genome and hg38 as your "new" genome
3. Change "Minimum ratio of bases that must remap" to 0.80
4. Paste your region (chr15:22,572,276-23,506,059) into the box
5. Click "submit"
6. Under "Results" click "View conversions". There should be one result, chr15:22367037-23226874.

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.

---

Matthew Speir

UCSC Genome Browser, User Support

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[Jing Zhang]

Hi, Matthew,

 

Thank you very much for your help!

 

Best,

 

Jing

 

From: Matthew Speir <msp...@ucsc.edu>
Sent: Tuesday, December 3, 2024 6:36 PM
To: Jing Zhang <Jing....@garudatx.com>
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] LiftOver for Chr15

 

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