Request for liftOver chain files

Si-Nan Zhai

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Nov 19, 2024, 12:58:41 PM11/19/24

to gen...@soe.ucsc.edu

Hi,

Dear colleague,

I am writing to request your kind assistance in creating several liftOver chain files. These files are crucial for our research as we need to convert genome positions from human (hg38) to the following species:

Crab-eating macaque (Macaca_fascicularis_6.0/GCA_011100615.1)
Gallus gallus (GRCg7b/GCA_016699485.1)
Papio anubis (Panubis1.0/GCA_008728515.1)
Macaca nemestrina (Mnem_1.0/GCA_000956065.1)
Sooty mangabeys (Caty_1.0/GCA_000955945.1)
Canis lupus familiaris (ROS_Cfam_1.0/GCA_014441545.1)
White-tufted-ear marmoset (mCalJac1.pat.X/GCA_011100555.1)

I sincerely appreciate your time and expertise in helping with this request. Your assistance will greatly facilitate our research. Please let me know if you need any additional information from my side.

With deepest gratitude,

Si-Nan Zhai
Ph.D Candidate,
Bioinformatics and Interdisciplinary Technologies (BITs), Li Yang’s Lab
(Former CAS-MPG Partner Institute for Computational Biology)
Shanghai Institute of Nutrition and Health
Chinese Academy of Sciences
320 Yue-Yang Road,
Shanghai 200031, China

Web:https://yanglab.github.io/
http://yang-laboratory.com

Matthew Speir

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Dec 3, 2024, 11:25:41 AM12/3/24

to Si-Nan Zhai, gen...@soe.ucsc.edu

Hello, Si-Nan.

Thank you for your request for LiftOver files.

For some of the requested accessions we only had the RefSeq assembly (i.e. starting with GCF rather than GCA) and for others the requested accession had since been superseded by a newer version (e.g. GCA_011100555.1 -> GCA_011100555.2). These files are now available on our download server:

Crab-eating macaque (Macaca_fascicularis_6.0/GCA_011100615.1)

Gallus gallus (GRCg7b/GCF_016699485.1)

Papio anubis (Panubis1.0/GCF_008728515.1)

Macaca nemestrina (Mnem_1.0/GCF_000956065.1)

Sooty mangabeys (Caty_1.0/GCF_000955945.1):

Canis lupus familiaris (ROS_Cfam_1.0/GCF_014441545.1)

White-tufted-ear marmoset (mCalJac1.pat.X/GCA_011100555.2)

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

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Laura Blanco-Berdugo

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Dec 10, 2024, 12:25:34 PM12/10/24

to UCSC Genome Browser Public Support

Hello, we are currently facing some challenges in generating chain files for several classic laboratory strains and would greatly appreciate your assistance with this process.

Would you be able to help us with creating these files? Your support would be immensely valuable to us.

We are needing a chain file using mm39 reference genome. Below is a list of the assemblies we need.

SPRET (https://www.ebi.ac.uk/ena/browser/view/GCA_921997135.2)

129 (https://www.ebi.ac.uk/ena/browser/view/GCA_001624185.1)

AJ (https://www.ebi.ac.uk/ena/browser/view/GCA_001624215.1)
CAST(https://www.ebi.ac.uk/ena/browser/view/GCA_001624445.1)
DBA(https://www.ebi.ac.uk/ena/browser/view/GCA_001624505.1)
NOD (https://www.ebi.ac.uk/ena/browser/view/GCA_001624675.1)
NZO (https://www.ebi.ac.uk/ena/browser/view/GCA_001624745.1)
PWK(https://www.ebi.ac.uk/ena/browser/view/GCA_001624775.1)
WSB(https://www.ebi.ac.uk/ena/browser/view/GCA_001624835.1)

Once again thank you very much for your time and help.

Laura Blanco-Berdugo

Hiram Clawson

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Dec 10, 2024, 4:45:50 PM12/10/24

to Laura Blanco-Berdugo, UCSC Genome Browser Public Support

Good Morning Laura:

A couple of those are available at this time:

https://hgdownload.soe.ucsc.edu/hubs/GCA/001/624/445/GCA_001624445.1/liftOver/GCA_001624445.1ToMm39.over.chain.gz

https://hgdownload.soe.ucsc.edu/hubs/GCA/001/624/835/GCA_001624835.1/liftOver/GCA_001624835.1ToMm39.over.chain.gz

https://hgdownload.soe.ucsc.edu/hubs/GCA/001/624/775/GCA_001624775.1/liftOver/GCA_001624775.1ToMm39.over.chain.gz

https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCA_001624445.1.over.chain.gz

https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCA_001624835.1.over.chain.gz

https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToGCA_001624775.1.over.chain.gz

Will take a look at the others.

--Hiram

Hiram Clawson

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Dec 18, 2024, 8:50:21 PM12/18/24

to Hiram Clawson, Laura Blanco-Berdugo, UCSC Genome Browser Public Support

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