Lift-over coordinates from one reference genome version to another

Locally and confidentially

You can lift over coordinates using the Jim Kent liftover tool. Download it from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/.

• liftOver but keep header track line (from IGV track file)

sed -e "s/^track /#track /; s/^browser /#browser/" customTrackBedFile.txt \
	| liftOver stdin map.chain stdout unMapped \
	| sed -e "s/^#track/track/; s/^#browser/browser/" > liftedCustomTrackBedFile.txt

See also: http://genomewiki.ucsc.edu/index.php/LiftOver_Howto

On the web

Two places are available for web-gui liftOver

• Galaxy Lift-Over - a graphical user interface of liftOver.
• NCBI map (see also their video)