GRCz12 liftover

[Lawson, Nathan]

Hi, 

I am starting to use the new GRCz12 assembly for zebrafish (https://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_6654484_GCF_049306965.1). I have remapped a number of RNA-seq datasets onto the new build, but it would be very helpful to be able to lift over various annotations from GRCz11. Unfortunately, I could not locate the required files.

Would it be possible for you to generate the necessary chain files to allow liftover from zebrafish GRCz11 to GRCz12? 

Also, is there any planned date for “official” release (with a full set of annotations) of GRCz12 on the UCSC site?

Thanks,

Nathan

Nathan D. Lawson, Ph.D.
Professor
Department of Molecular, Cell, and Cancer Biology
University of Massachusetts Medical School 
364 Plantation Street
LRB617
Worcester, MA 01605
website: lawsonlab.umassmed.edu
email: nathan...@umassmed.edu
twitter: @LawsonZFLab
phone: 508-856-1177

[Matthew Speir]

Hello, Nathan.

Thank you for your LiftOver file request.

These files are now available on our download server:

• https://hgdownload.gi.ucsc.edu/hubs/GCF/049/306/965/GCF_049306965.1/liftOver/GCF_049306965.1ToDanRer11.over.chain.gz
• https://hgdownload.gi.ucsc.edu/goldenPath/danRer11/liftOver/danRer11ToGCF_049306965.1.over.chain.gz

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.

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Matthew Speir

UCSC Genome Browser, User Support

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[Lawson, Nathan]

Great! Thanks - I will give these a try.