[Genome] file conversion

[Brooke Rhead]

Hi again Beate,

A colleague suggested a couple of things to double-check:

1. Make sure that the input coordinates in test1_2003.txt really are from hg16.
2. Make sure you are using our 0-based half-open coordinates in the input bed file given to liftOver (See an explanation here: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1).

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Brooke Rhead wrote:
> 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
>> Canynge Hall
>> Room 3.5
>> Whiteladies Road
>> Bristol BS8 2PR
>> UK
>>
>> ++44-117-331-3901
>>
>>
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>>   
>>     
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