[Genome] there might have some bug in your liftover batch program?

[Ann Zweig]

Hello Zxu,

	There is a 50,000 bp telomeric gap at the very beginning of chr11 in both 
assemblies.  The liftOver tool skips over this gap.

Gap Type: telomere
Bridged: no
Position: chr11:1-50000
Band: 11p15.5
Genomic Size: 50000


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


zxu wrote:
> hi,
> 
> might have some bug in your liftover batch program?
> I am trying to conver 2004 Human version to 2006 Human version. when convert
> chr11:1-1000000, it give back result chr11:50001-1000000, missing 50000 bp. for
> all other conversion, it seems OK.
> 
> zd
> TWRI
> UHN, U of toronto
> 
> Ann Zweig wrote:
> 
>> Hello zxu,
>>
>>         It is possible to do what you are suggesting by making a Custom Track
>> from the refSeq track.  When you do this, you can limit the genes you
>> would like to display in your track.
>>
>>         If you have never made a Custom Track using the Table Browser, you can
>> read about it here: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
>>
>>         Configure the Table Browser by choosing the refSeq table.  Then enter
>> your list of genes into the 'identifiers (names/accessions): "paste
>> list"' (e.g. DUSP22 IRF4).  Choose "custom track" as your output format.
>>   Then follow the prompts to view your newly-created Custom Track in the
>> Genome Browser.
>>
>>         I hope this information is helpful to you.  Please don't hesitate to
>> contact the mail list again if you require further assistance.
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>> Please feel free to search the Genome mailing list archives by visiting
>> our home page, clicking on "Contact Us", then typing a word or phrase
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>> mailing list.
>>
>> zxu wrote:
>>> I had a question about how to customize refseq track?  bacically, I want
>>> to show certain refseq within certain chromosome  but not all of them?
>>> let's say in chr6:200000-1000000, there are gene DUSP22, IRF4, EXOC2,
>>> HUS1B.  but I want to only show DUSP22, IRF4, not the other two genes.
>>> since  DUSP22, IRF4 are realted to IFN pathway, let's say?
>>>
>>> Best regrads
>>>
>>> zd
>>>
>>>
>>>
>>>
>>> _______________________________________________
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