Liftover chain file for the latest sheep reference genome (Oar_rambouillet_v1.0)

[Ruidong Xiang]

Dear Colleagues,

We are working on the genomics of ovine and it has come to a need to integrate results previously generated on sheep reference genome ISGC Oar_v4.0 with the results generated on the latest Oar_rambouillet_v1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_002742125.1/). As far as we know a standard procedure is to liftover coordinates from the old genome to the new genome, but we cannot find the chain files needed for liftover for Oar_rambouillet_v1.0. 

In fact on the UCSC website the latest chain file for sheep is from 2015. We are wondering if there are ways that we can retrieve the chain files of Oar_rambouillet_v1.0? Or any suggestions regarding converting coordinates from old to new sheep genome would also be very helpful.

Many thanks for the help.

Best Regards,

Ruidong

Ruidong Xiang, Ph.D;

Research Fellow, Computational Biology;

Faculty of Veterinary and Agricultural Sciences;

The University of Melbourne;

Parkville VIC 3010, Australia;

+61 03 9032 7251.

[Gerardo Perez]

Hello Dr. Ruidong Xiang,

Thank you for your interest in the Genome Browser.

We have made the files available on our download server:

GCF_002742125.1 → oviAri4: https://hgdownload.soe.ucsc.edu/goldenPath/GCF/002/742/125/GCF_002742125.1/liftOver/GCF_002742125.1ToOviAri4.over.chain.gz

oviAri4 → GCF_002742125.1: https://hgdownload.soe.ucsc.edu/goldenPath/oviAri4/liftOver/oviAri4ToGCF_002742125.1.over.chain.gz

The GCF_002742125.1 to oviAri4 Chain/Net tracks can be visualized here:
https://genome.ucsc.edu/h/GCF_002742125.1

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.

Gerardo Perez
UCSC Genomics Institute

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