[Genome] file conversion

[Brooke Rhead]

Hello Beate,

Do you get a similar result if you use our web-based BLAT to convert 
coordinates from hg16 to hg18?
http://genome.ucsc.edu/cgi-bin/hgBlat

If you get a better result using web-based BLAT, instructions for 
replicating results using command-line BLAT are here: 
http://genome.ucsc.edu/FAQ/FAQblat#blat7 .

If you are still having troubles, can you send us an example of hg16 
coordinates that do not seem to be lifting correctly to hg18?

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Beate Glaser wrote:
> Hi,
>
> I tried to convert some human methylation data (BED file format) given in 
> hg16 (July 2003) coordinates into hg 18 coordinates (March 2006) using :
>
> liftOver.linux.i386 test1_2003.txt hg16ToHg18.over.chain test1_2006.txt 
> UnMapped
>
> The conversion under linux is carried out however, the alignment is wrong. 
> I only know because the methylation position is always C in hg16 (+ strand) 
> and its all over the place in hg18. Would anyone know what went wrong?
>
> Thanks a lot for any help.
>
> Beate
>
> ----------------------
> Beate Glaser
> Dept Social Medicine
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>
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>
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