[Genome] (no subject)

[Swapan Mallick]

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
---------------------------------------------------------