Dear Dr. Pages.

       Thank you very much for your quick reply.

Ping


2010/6/18 Hervé Pagès <hpages@fhcrc.org>

> Hi Ping,
>
>
> Ping Ma wrote:
>
>> Dear Dr. Pages,
>>
>>   I am learning the GenomicRanges in bioconductor. I followed your notes
>> to do some excise.
>>  My question is whether I can use makeTranscriptDbFromUCSC
>>
>>  to get relevant gene annonation of */Sulfolobus solfataricus P2/*
>> http://archaea.ucsc.edu/cgi-bin/hgGateway?db=sulSol1
>>
>
> Unfortunately this is not supported at the moment.
>
> The makeTranscriptDbFromUCSC() function is defined in the
> GenomicFeatures package. I just added the 'url' and 'goldenPath_url'
> arguments to it, so, *in theory*, the user now should be able to
> specify the location of an alternate browser.
>
> The default values for these arguments are:
>  url="http://genome.ucsc.edu/cgi-bin/"
>  goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath"
> so, by default, makeTranscriptDbFromUCSC() is using the browser
> at Santa Clara.
>
> To use another browser (e.g. one of the mirror listed on
> http://genome.ucsc.edu/mirror.html), one would need to do
> something like:
>
>  > makeTranscriptDbFromUCSC(genome="sacCer2",
>      tablename="ensGene",
>      url="http://genome.hmgc.mcw.edu/cgi-bin/")
>  Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
>
> The problem is that I get this error with all the browser mirrors
> I tried. I don't know if it's an issue with the configuration of
> the remote browser, or with the rtracklayer::browserSession()
> function that is used behind the scene by makeTranscriptDbFromUCSC()
> to connect to the remote Genome Browser:
>
>  > library(rtracklayer)
>  > session <- browserSession(url="http://genome.hmgc.mcw.edu/cgi-bin/")
>  Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie
>
> I'm cc'ing Michael Lawrence, the author and maintainer of rtracklayer.
>
> Cheers,
> H.
>
>
>
>>  Thank you very much.
>>
>> Best,
>>
>> Ping
>>
>>
>> --
>> Ping Ma
>> Assistant Professor, Department of Statistics
>> Faculty Member, Institute for Genomic Biology  University of Illinois at
>> Urbana-Champaign
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
Ping Ma
Assistant Professor, Department of Statistics
Faculty Member, Institute for Genomic Biology
University of Illinois at Urbana-Champaign

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