Conversion Between Hg18 And Hg19

Question

[Perry]

I want to draw chromosome ideogams with chromosome location data. I'm using the quantsmooth library in R, as described in this BioStar question. The quantsmooth plots are for hg18, but my data are for hg19. Is there an easy way to convert my hg19 chromosome positions to hg18 positions?

I'm looking for an existing map (hg19 chr 1, base 25 -> hg18 chr 1, base 20), or a conversion formula.

[Malachi Griffith]

This post describes various tools for coordinate conversions: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)

Answer 1

[brentp]

Have a look at this question which references liftOver.

Answer 2

[Ian]

FYI there is also an implementation of liftOver in Galaxy. See 'Lift-Over' on the left hand tools panel.