Request chain file between ARS-UCD1.2 (GCA_002263795.2) and ASM3988116v1 (GCA_039881165.1)

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Aixin Li

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Oct 17, 2024, 12:11:16 PM10/17/24
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Dear UCSC Genome Browser Group,
I would like to extend my sincere gratitude for your team's invaluable support in our scientific research endeavors. Currently, I am investigating the impact of group-specific reference genomes on variant identification. To proceed with my study, I require assistance with two genome coordinate conversions. Initially, I need to convert coordinates from ARS-UCD1.2 (GCA_002263795.2) to ASM3988116v1 (GCA_039881165.1). Subsequently, I also need to revert a portion of  coordinates back to ARS-UCD1.2 (GCA_002263795.2) from ASM3988116v1 (GCA_039881165.1).
I have attempted to create the necessary chain files, but unfortunately, I have been unsuccessful. I am hopeful that your team can assist us in generating these two chain files. Any suggestions or guidance you could provide would be greatly appreciated.
Thank you for your attention to this matter.
Best regards,
Aixin





Clay Fischer

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Oct 29, 2024, 3:11:10 PM10/29/24
to Aixin Li, genome
Dear Aixin,

Our engineer has generated chain files. They commented that GCA_002263795.2 is what we call bosTau9 and the alignment has been done to that.

You can download these chain files using the following directories:
https://hgdownload.soe.ucsc.edu/hubs/GCA/039/881/165/GCA_039881165.1/liftOver/
https://hgdownload.soe.ucsc.edu/hubs/GCF/002/263/795/GCF_002263795.3/liftOver/

Thanks,
--
Clay Fischer
UCSC Genomics Institute

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Aixin Li

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Nov 1, 2024, 7:08:02 PM11/1/24
to Clay Fischer, genome

Dear UCSC Genome Browser Group,

I truly appreciate the assistance and support provided by your team. I apologize for the inconvenience of reaching out once more. While reviewing the link you provided, I noticed the file named GCF_002263795.3ToGCF_000767855.1.over.chain.gz. Unfortunately, I am unable to utilize this chain file as my variant calling was based on ARS-UCD1.2 (GCA_002263795.2), not ARS-UCD2.0 (GCF_002263795.3). I am hopeful that your team can assist us in generating a chain file from ARS-UCD1.2 (GCA_002263795.2), which you refer to as bosTau9, to ASM3988116v1 (GCA_039881165.1). Your help in this matter is greatly appreciated.

Thank you for your attention to this matter.

Best regards,

Aixin








Original:

Jairo Navarro Gonzalez

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Nov 1, 2024, 7:55:36 PM11/1/24
to Aixin Li, Clay Fischer, genome

Hello,

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

The two assemblies versions (GCA_002263795.2 and GCA_002263795.3) for bosTau9 are identical in terms of sequence, with the exception of sequence names and the lack of chrMT in GCA_002263795.2.

You can convert the sequence names for GCA_002263795.3 in the liftOver chain file or the annotation file to match the names of GCA_002263795.2. Using the chromosome alias file, you can convert the sequence names from the .3 version (first column in the file) to the .2 version (third column in the file:

https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.chromAlias.txt

Here are the first few lines from that file:

# ucsc    ensembl    genbank    refseq
chr1    1    CM008168.2    NC_037328.1
chr10    10    CM008177.2    NC_037337.1
chr11    11    CM008178.2    NC_037338.1

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.

Jairo Navarro
UCSC Genome Browser


To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/AL6AUQBKIZd4XD7*bBmhuqpR.2.1730444552803.Hmail.liaixin%40nwafu.edu.cn.

Aixin Li

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Nov 4, 2024, 1:20:30 PM11/4/24
to Jairo Navarro Gonzalez, genome
Dear UCSC Genome Browser Group,
I would like to extend my sincere gratitude for your team's help. Thank you very much !

Best regards,

Aixin









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