USCS LiftOver Queries

[周亚琦]

Dear UCSC Genome Browser Team,

I hope this email finds you well. Thank you very much for your team’s invaluable support of scientific research.

I am currently working on a project that requires the conversion of genomic coordinates. However, I was unable to locate the relevant chain file for this conversion on the UCSC Genome Browser.

Specifically, I found that the following chain files have not yet been created:

 

goat (ARS1.2,GCF_001704415.2) to domestic yak (BosGru3.0,GCA_005887515.2)

sheep ( ARS-UI_Ramb_v2.0, GCF_016772045.1) to domestic yak (BosGru3.0,GCA_005887515.2)

domestic yak (BosGru3.0,GCA_005887515.2) to goat (ARS1.2,GCF_001704415.2) 

domestic yak (BosGru3.0,GCA_005887515.2) to sheep ( ARS-UI_Ramb_v2.0, GCF_016772045.1)

Would it be possible for your team to provide the chain file ?

Thank you for your help. I look forward to hearing from you.

 

Best regards,  

yaqi zhou

	周亚琦
zyq...@nwafu.edu.cn

[Gerardo Perez]

Hello,

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

We have a chain file available from GCF_001704415.2 (goat ARS1.2) to GCA_005887515.3 (domestic yak BosGru3.1): https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.2/liftOver/GCF_001704415.2ToGCA_005887515.3.over.chain.gz.

Please note that the GCA_005887515.2 (domestic yak BosGru3.0) assembly was marked as contaminated by GenBank and has been replaced by GCA_005887515.3: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_005887515.2/.

We also have a chain file from GCF_016772045.2 (sheep ARS-UI_Ramb_v3.0) to GCA_005887515.3 (domestic yak BosGru3.1): https://hgdownload.soe.ucsc.edu/hubs/GCF/016/772/045/GCF_016772045.2/liftOver/GCF_016772045.2ToGCA_005887515.3.over.chain.gz.

GenBank has updated the GCF_016772045.1 (sheep ARS-UI_Ramb_v2.0) assembly to GCF_016772045.2 as well: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016772045.1/.

Would either of these chain files work for your project?

I hope this is helpful. Please include genom...@soe.ucsc.edu in any replies to ensure visibility by the team.

Gerardo Perez
UCSC Genomics Institute

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