[BioC] question on makeTranscriptDbFromUCSC

[Hervé Pagès]

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

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