LiftOver chain file (build 38 --> 37)

[Sheir, Stephanie]

Dear UCSC team, 

I would like to use liftOver to convert from build 38 to 37. I attempted wget http://hgdownload.cse.ucsc.edu/goldenpath/hg38/liftOver/hg38ToHg19.over.chain.gz, but am not currently obtaining any results with a number of different files. Could you please confirm if this URL is the correct chain file for 38 to 37 (reverse from the usual conversion), and if not, could you please provide the correct file?

Kind regards,

Stephanie

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Stephanie Sheir

Soc-B CDT in Biosocial Research

UCL

[Matthew Speir]

Hello, Stephanie.

Thank you for your question about downloading LiftOver files from the UCSC Genome Browser.

The URL you provided works for me. But, the 'cse' subdomain has generally been deprecated by UCSC and we've since replaced it with 'gi'. Here's a URL that should work: https://hgdownload.gi.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz.

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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