How to convert a lot of hg18 coordinates to hg19 coordinates in a fast way?

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Yu, Jiamei

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Feb 21, 2013, 3:51:29 PM2/21/13

to gen...@soe.ucsc.edu

I want to know how to convert a lot of hg18 coordinates to hg19 coordinates in a fast way?

Thanks.

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Pauline Fujita

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Feb 21, 2013, 5:02:53 PM2/21/13

to Yu, Jiamei, gen...@soe.ucsc.edu

Hello,

You could use our liftover tool found here:

http://www.genome.ucsc.edu/cgi-bin/hgLiftOver

Note that pasted coordinates need to be in BED or chrN:start-end
format (see more about BED format here:
http://www.genome.ucsc.edu/FAQ/FAQformat.html#format1)

If you have a really large list of coodinates you might want to look
into downloading and using the liftover command line utility. To lift
genome annotations locally on Linux systems, download the liftOver
executable here:

http://hgdownload.cse.ucsc.edu/admin/exe/

and the appropriate chain file here:

http://hgdownload.cse.ucsc.edu/downloads.html#liftover

You can also run liftOver with no arguments to see the usage message.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu