[Genome] (no subject)

[Rachel Harte]

Hello,

Here is a link to where you can download the precompiled executables for
liftOver:

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

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Thu, 19 Apr 2007, Swapan Mallick wrote:

> Hello again,
>
> I have two questions:
>
> 1)
> By any chance do you have precompiled executables for: ia64 linux?
>
> Amazingly, we don't have mysql installed so compiling from source fails (
> at the point when jkhgap.a is being made ).
>
> Alternatively, is there a way of building liftOver without mysql. In the
> meantime I'm trying to get mysql installed but it may not be a quick
> process here.
>
> 2)
> Is there any detailed documentation on how liftOver works? Conceptually it
> sounds like it should be a trivial problem, but I'm sure there are many
> details I'm not aware of.
>
> We plan to process many billions of sequences which makes error checking
> non-trivial, and I'd like to know more about what any pitfalls might be.
>
>
> Shop
>
>
>
>
> > Hello Shop Mallick,
> >
> > To convert from hg16 to hg18 coordinates, you will only need to use one
> > liftOver chain file and that is hg16ToHg18.over.chain. You can download
> > this file from the downloads server by clicking on the link to LiftOver
> > files in the human hg16 section or go directly to:
> >
> > http://hgdownload.cse.ucsc.edu/goldenPath/hg16/liftOver/
> >
> > I hope that this helps you. Please let us know if you have further
> > questions.
> >
> > Rachel
> >
> > Rachel Harte
> > UCSC Genome Bioinformatics Group
> > http://genome.ucsc.edu
> >
> >
> > On Wed, 18 Apr 2007, Swapan Mallick wrote:
> >
> >> Hello,
> >>
> >> I'm working at the genetics department in the Harvard Medical School.
> >>
> >> We have a set of alignments which were created for version 16 of the
> >> human
> >> genome. We wish to map these to version 18, and I would like to build
> >> wrappers around the liftover tool to do this.
> >>
> >> I have already downloaded the chain file:
> >> hg18ToHg17.over.chain
> >>
> >> But I think I need the corresponding files: hg16ToHg18.over.chain . Is
> >> this available?
> >>
> >> Best regards,
> >> Shop Mallick
> >>
> >>
> >> ---------------------------------------------------------
> >> Dr Swapan 'Shop' Mallick
> >> Dept. of Genetics
> >> Harvard Medical School, NRB
> >> 77 Avenue Louis Pasteur
> >> Boston, MA 02115
> >> Tel: +1-617-432-5993
> >> Email: shop at genetics.med.harvard.edu
> >> ---------------------------------------------------------
> >>
> >> _______________________________________________
> >> Genome maillist  -  Genome at soe.ucsc.edu
> >> http://www.soe.ucsc.edu/mailman/listinfo/genome
> >>
> >
> >
>
>
> ---------------------------------------------------------
> Dr Swapan 'Shop' Mallick
> Dept. of Genetics
> Harvard Medical School, NRB
> 77 Avenue Louis Pasteur
> Boston, MA 02115
> Tel: +1-617-432-5993
> Email: shop at genetics.med.harvard.edu
> ---------------------------------------------------------
>