Inquiry regarding UCSC Chain Files

[Martina Tunjić]

Hi,

I need to convert data from Sus Scrofa 9 assembly to Sus Scrofa 11.1, would you be able to provide such chain file?

Thank you in advance.

Kind regards,

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Martina Tunjić, mag.ing.agr. | M. Sc. Agri.

Sveučilište u Zagrebu Agronomski fakultet  | University of Zagreb Faculty of Agriculture

Odsjek za biljne znanosti | Division of Plant Science

Zavod za oplemenjivanje bilja, genetiku i biometriku | Department of Plant Breeding, Genetics and Biometrics

Svetošimunska cesta 25

HR – 10000 Zagreb, Hrvatska

Tel.: +385 1 2393 111

Mob.: +385 99 804 5305

E-mail: mtu...@agr.hr

www.agr.unizg.hr 

[Matthew Speir]

Hello, Martina. 

Thank you for your LiftOver file request. 

The files are available at these links:
susScr2 -> susScr11: https://hgdownload.soe.ucsc.edu/goldenPath/susScr2/liftOver/susScr2ToSusScr11.over.chain.gz
susScr11 -> susScr2: https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/liftOver/susScr11ToSusScr2.over.chain.gz

Chain coverage (% of genome covered by alignments):
susScr2 -> susScr11: 99.414%
susScr11 -> susScr2: 97.976%

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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