LiftOver Tool

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Shailesh Sharma

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Feb 20, 2025, 11:58:42 AM2/20/25
to gen...@soe.ucsc.edu

Dear Sir,
We have a bed file of Bos taurus from the latest Genome assembly ARS-UCD2.0 but the liftover tool has ARS-UCD1.2 (as latest in it). We want to convert the bed file of ARS-UCD2.0 to mouse genomic coordinates. Can you please guide us?

Thanks
Shailesh 





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धन्यवाद एवं शुभकामनाएँ/Thanks and Regards,

डॉ शैलेश शर्मा/ Dr Shailesh Sharma

वैज्ञानिक-ई / Scientist-E 

ब्रिक-राष्ट्रीय पशु जैव प्रौद्योगिकी संस्थान (एन आई ऐ बी)

BRIC-National Institute of Animal Biotechnology (NIAB)
जैव प्रौद्योगिकी विभाग, विज्ञान और प्रौद्योगिकी मंत्रालय, भारत सरकार
Department of Biotechnology, Ministry of Science and Technology, GoI

Opp. Journalist Colony, Near Gowlidoddy,
Extended Q City Road, Gachibowli,
Hyderabad, Telangana, India

PIN: 500 032 
Office: +91-040-23120119
liftover.png

Gerardo Perez

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Mar 5, 2025, 7:11:38 PM3/5/25
to Shailesh Sharma, gen...@soe.ucsc.edu

Hello, Shailesh.

Thank you for your interest in the Genome Browser and for your question about the LiftOver tool.

We offer liftOver as a utility to move annotations in bed format from GCF_002263795.3 (ARS-UCD2.0) to mm39. You can download the ‘liftOver’ utility from the downloads page, https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads. You can then find liftOver under the directory that matches your operating system. For example, here is the direct link for Linux: https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver

You can then run liftOver as the following:

$ ./liftOver input.bed GCF_002263795.3ToMm39.over.chain output.bed unMapped

The GCF_002263795.3 to mm39 over.chain file is available on our downloads server: https://hgdownload.soe.ucsc.edu/hubs/GCF/002/263/795/GCF_002263795.3/liftOver/GCF_002263795.3ToMm39.over.chain.gz

The mm39 to GCF_002263795.3 (ARS-UCD2.0) over.chain file can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCF_002263795.3.over.chain.gz

You can run a utility on its own to see a help message, e.x.

$ ./liftOver
liftOver - Move annotations from one assembly to another
usage:
   liftOver oldFile map.chain newFile unMapped
oldFile and newFile are in bed format by default, but can be in GFF and
maybe eventually others with the appropriate flags below.
The map.chain file has the old genome as the target and the new genome
as the query.

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


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Shailesh Sharma

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Mar 10, 2025, 4:30:48 PM3/10/25
to Gerardo Perez, gen...@soe.ucsc.edu
THank yOu. Let us try. I will write again soon. Shailehs 

Shailesh Sharma

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Mar 10, 2025, 4:31:34 PM3/10/25
to Gerardo Perez, gen...@soe.ucsc.edu
Hello,

Thank you for the response. The above chain file is working with Mice and we got the desirable results. Now we wish to check with the other livestock species like pig, sheep, goat, buffalo and chicken. Can you pls tell the process to generate chain file or can you guide how to generate chain file for above mentioned five species with the same latest GCF_002263795.3 (ARS-UCD2.0). 

Shailesh 





On Thu, Mar 6, 2025 at 5:41 AM Gerardo Perez <gpe...@ucsc.edu> wrote:

Jairo Navarro Gonzalez

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Mar 13, 2025, 7:03:39 PM3/13/25
to Shailesh Sharma, gen...@soe.ucsc.edu, Gerardo Perez

Hello,

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

To assist you further, can you please also send us the assembly IDs for each of these organisms? Without the assembly IDs, we do not know which assembly you need for the liftOver files.

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 Genome Browser


To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAH94JhUhVEjOLus4XgoxjGtp0fPHi%3DUtKaon2zzwR9Uc746nfA%40mail.gmail.com.

Shailesh Sharma

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Mar 25, 2025, 12:44:04 PM3/25/25
to Jairo Navarro Gonzalez, emmanuel raj, Anjali mishra, Dushyant Deotale, gen...@soe.ucsc.edu, Gerardo Perez
Thank you for your email. I was at PAG Asia in Delhi. The assembly  ids for the following species is following:

1. Bubalus bubalis (water buffalo) -  NDDB_SH_1 (GCF_019923935.1)
2. Capra hircus (goat) - ARS1.2 (GCF_001704415.2)
3. Ovis aries (sheep) -ARS-UI_Ramb_v3.0 (GCF_016772045.2)
4. Sus scrofa (Pig) -  Sscrofa11.1 - (GCF_000003025.6)
5. Gallus gallus (Chicken) - bGalGal1.mat.broiler.GRCg7b (GCF_016699485.2)

Do let me know in case we can work in collaboration.


Shailesh 

Matthew Speir

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Apr 7, 2025, 12:06:26 PM4/7/25
to Shailesh Sharma, Jairo Navarro Gonzalez, emmanuel raj, Anjali mishra, Dushyant Deotale, gen...@soe.ucsc.edu, Gerardo Perez
Hello, Shailesh.

These files are available on our download server:


1. Bubalus bubalis (water buffalo) - NDDB_SH_1 (GCF_019923935.1)


2. Capra hircus (goat) - ARS1.2 (GCF_001704415.2)


4. Sus scrofa (Pig) - Sscrofa11.1 - (GCF_000003025.6)


5. Gallus gallus (Chicken) - bGalGal1.mat.broiler.GRCg7b (GCF_016699485.2)

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


To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAD8LMEMxJgZ1YFi1MtmUwjBa6YFTm-kUF%2BOfvT7cFZm1aHsZ1A%40mail.gmail.com.

Dushyant Deotale

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May 1, 2025, 11:59:29 AM5/1/25
to cc: Jairo Navarro Gonzalez, gen...@soe.ucsc.edu, Gerardo Perez, emmanuel raj, Shailesh Sharma, Anjali mishra


---------- Forwarded message ---------
From: Dushyant Deotale <dushyant....@gmail.com>
Date: Wed, Apr 30, 2025 at 5:48 PM
Subject: Re: [genome] LiftOver Tool
To: Shailesh Sharma <shailes...@niab.org.in>


Hello, liftover tool team

We want to know the basic algorithm of the LiftOver tool to understand how it works and how it gives output.
We were working on the Cattle genome. So, as we required the latest buffalo genome chain file, we contacted you.

*What we have done
We have blasted the cattle circRNA onto the buffalo genome. As a result, we have got the information where the sequence of interest is mapping or getting hits. So we confirmed that the sequence of interest is somewhat conserved in buffalo, and so in goat.
After applying some filters, we have confirmed hits of cattle cirRNA on buffalo and goat genomes. So I think this step itself validates conserved circRNA in different animals. which we faced lag in the leftover tool. (In the attached screenshot, you can see the result of BLAST and after applying filters)
image.png

We have some doubt regarding the algorithm of the tool:
1. Based on only the genome coordinates of cattle, how can you tell the position/coordinate of buffalo, as the tool is not asking for a FASTA sequence as input?

please rectify our doubts.

Thanking You 


Best Resgards
Dushyant Deotale
PA-I
NIAB, Hyderabad

  



On Wed, Apr 30, 2025 at 2:51 PM Shailesh Sharma <shailes...@niab.org.in> wrote:
WHAT YOU ALREADY DID. pLS EXPLAIN WITH ATLEST 2-3 FIGURES AND TABLES 

On Wed, Apr 30, 2025 at 2:40 PM Dushyant Deotale <dushyant....@gmail.com> wrote:
hello, liftover tool team
We want to know the basic algorithm of the LiftOver tool to know how it works and how it gives output.


On Tue, Apr 29, 2025 at 2:26 PM Shailesh Sharma <shailes...@niab.org.in> wrote:
Dushyant pls update me 

On Mon, Apr 21, 2025 at 2:50 PM Shailesh Sharma <shailes...@niab.org.in> wrote:
Dushyant pls update me 

On Mon, Apr 7, 2025 at 10:13 PM Shailesh Sharma <shailes...@niab.org.in> wrote:
Please have a look 

Gerardo Perez

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May 21, 2025, 12:57:51 PM5/21/25
to Dushyant Deotale, gen...@soe.ucsc.edu, emmanuel raj, Shailesh Sharma, Anjali mishra

Hello, Dushyant.

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

The core of the LiftOver algorithm is based on projecting coordinates through precomputed alignment data between two species’ genomes. In this case, the projection occurs between cattle and buffalo. The tool relies on chain and net alignment files, which describe how regions in one genome align to another. Because these alignments are precomputed, the tool does not require a FASTA sequence as input.

However, the process becomes more complex when dealing with features that have a block structure, such as transcripts with exons and introns, or when only part of a region maps. For example, only the start or end of a region may align successfully. The tool also offers advanced options like -multiple and -ends, which influence how mappings are handled.

Generating whole-genome alignments (chains and nets) is a significantly more complex process than the coordinate conversion that LiftOver performs. If you are interested in how these alignments are generated, we recommend reviewing the following paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/.

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

Dushyant Deotale

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May 22, 2025, 12:52:17 PM5/22/25
to Gerardo Perez, gen...@soe.ucsc.edu, emmanuel raj, Shailesh Sharma, Anjali mishra
Hello team Liftover,

Thank you for getting back to me. 
I will go through the attached research article. If I have any doubts, I will convey them to you.

Thank You

Best Regards
Dushyant Deotale

Shailesh Sharma

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May 22, 2025, 12:52:22 PM5/22/25
to Dushyant Deotale, Gerardo Perez, gen...@soe.ucsc.edu, emmanuel raj, Anjali mishra
Team Liftover is very supportive. thanks 
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