Canine ROS_Cfam_1.0 assembly

[Antonella Fanelli]

Dear all,

I would like to ask you if it is possible to add the canine ROS_Cfam_1.0 assembly to the dog  genome browser.

This is now considered the reference genome for dog and many resources are only available in ROS_Cfam_1.0. To the best of my knowledge, the NCBI Genome Remapping Service was the only way to convert genomic coordinates from CanFam3 to ROS and vice versa, but it's no longer available.

Adding this assembly would be a great help to those working with the dog genome.

Many regards

Antonella Fanelli

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Dr.ssa Antonella Fanelli, MSc, PhD

Dipartimento di Scienze Veterinarie

Università degli Studi di Torino

Largo Paolo Braccini, 2, 10095, Grugliasco (TO)

+39 011 670 9037

[Jairo Navarro Gonzalez]

Hello,

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

You can find the ROS_Cfam_1.0 genome assembly available as a GenArk hub. The assembly hub has a canFam3 chain/net track that shows alignments between the two assemblies:

https://genome.ucsc.edu/h/GCF_014441545.1

You can download the liftOver files to perform the coordinate conversions from the following directory:

ROS_Cfam_1.0:

https://hgdownload.soe.ucsc.edu/hubs/GCF/014/441/545/GCF_014441545.1/liftOver/

canFam3 --> ROS_Cfam_1.0:

https://hgdownload.soe.ucsc.edu/goldenPath/canFam3/liftOver/canFam3ToGCF_014441545.1.over.chain.gz

If you are unfamiliar with performing LiftOver conversions, you can learn more from these help pages. You can also search the mailing list archive for previously answered questions:

LiftOver documentation:

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert

LiftOver command-line example:

https://genome.ucsc.edu/FAQ/FAQdownloads.html#liftOver

LiftOver mailing list questions:

https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=LiftOver

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

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