Re: Re: [genome-www] Liftover Chain Files for Eurasian tree sparrow and Chicken genome

[chen...@ioz.ac.cn]

Many thanks to your help!

But the sparrow genome (GCF_014805655.1) is not what I am using, could I provide with another sparrow genome (in private link maybe)?

Best regards,

Yilin

-----原始邮件-----
发件人:"Jairo Navarro Gonzalez" <jnav...@ucsc.edu>
发送时间:2024-10-08 08:26:24 (星期二)
收件人: chen...@ioz.ac.cn
抄送: genom...@soe.ucsc.edu
主题: Re: [genome-www] Liftover Chain Files for Eurasian tree sparrow and Chicken genome

Hello,

Thank you for using the UCSC Genome Browser and requesting these liftOver files.

You can now find these files available for download using the following URLs:

Chicken white leghorn layer X broiler to Eurasian tree sparrow:

https://hgdownload.soe.ucsc.edu/hubs/GCF/016/699/485/GCF_016699485.2/liftOver/GCF_016699485.2ToGCF_014805655.1.over.chain.gz

Eurasian tree sparrow to Chicken white leghorn layer X broiler:

https://hgdownload.soe.ucsc.edu/hubs/GCF/014/805/655/GCF_014805655.1/liftOver/GCF_014805655.1ToGCF_016699485.2.over.chain.gz

You can also view these tracks on the genome assemblies:

https://genome.ucsc.edu/h/GCF_016699485.2 (chicken white leghorn layer X broiler)
https://genome.ucsc.edu/h/GCF_014805655.1 (Eurasian tree sparrow)

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

On Mon, Sep 23, 2024 at 2:47 AM <chen...@ioz.ac.cn> wrote:

Dear Genome Browser team,

I'm currently working on a small Passeriformes - the Eurasian tree sparrow Passer montanus.

I would like to ask if you could kindly help preparing liftover chain files from Chicken (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/) to the tree sparrow, and vice versa? 

Because the tree sparrow genome has not been pubulished, what kind of file should I need to provide?

Thank you very much.

Best regards, 

Yilin

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[Matthew Speir]

Hi, Yilin.

We only work with genomes that have been published in NCBI per agreements with other genome browsers. We provide instructions on how you can create your own LiftOver files here: https://genomewiki.ucsc.edu/index.php?title=DoBlastzChainNet.pl.

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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