UCSC: convert from hg18 to hg19 - rtracklayer?
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.9 years ago
Hi, I had a set of regions (e.g. 'chr7:94282859-94288530') from hg18 that I want to convert to hg19. Is there a way that I can do this in rtracklayer (or any other package)? thanks! [[alternative HTML version deleted]]
rtracklayer rtracklayer • 2.7k views
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@sean-davis-490
Last seen 12 weeks ago
United States
On Mon, May 2, 2011 at 9:05 PM, Tim Smith <tim_smith_666@yahoo.com> wrote: > Hi, > > I had a set of regions (e.g. 'chr7:94282859-94288530') from hg18 that I > want to > convert to hg19. Is there a way that I can do this in rtracklayer (or any > other > package)? > > Hi, Tim. http://genome.ucsc.edu/cgi-bin/hgLiftOver This is available as an executable that you could wrap using R, but it is pretty easy to use the online version. Sean [[alternative HTML version deleted]]
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Thanks Sean! That worked. ________________________________ From: Sean Davis <sdavis2@mail.nih.gov> Cc: bioc <bioconductor@stat.math.ethz.ch> Sent: Mon, May 2, 2011 9:25:10 PM Subject: Re: [BioC] UCSC: convert from hg18 to hg19 - rtracklayer? Hi, > >I had a set of regions (e.g. 'chr7:94282859-94288530') from hg18 that I want to >convert to hg19. Is there a way that I can do this in rtracklayer (or any other >package)? > > Hi, Tim. http://genome.ucsc.edu/cgi-bin/hgLiftOver This is available as an executable that you could wrap using R, but it is pretty easy to use the online version. Sean [[alternative HTML version deleted]]
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@michael-lawrence-3846
Last seen 8 months ago
United States
On Mon, May 2, 2011 at 6:05 PM, Tim Smith <tim_smith_666@yahoo.com> wrote: > Hi, > > I had a set of regions (e.g. 'chr7:94282859-94288530') from hg18 that I > want to > convert to hg19. Is there a way that I can do this in rtracklayer (or any > other > package)? > > Hi, rtracklayer has native support for lift-over. Use import.chain to bring in a UCSC chain file and then call the liftOver function. See ?liftOver. This is a lot faster than the UCSC executable (in my tests), and it has a commercial-friendly license. Michael > thanks! > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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