[BioC] TranscriptDB object

[Hervé Pagès]

Hi Assa,

On 11-07-28 07:58 AM, Assa Yeroslaviz wrote:
> Hi,
>
> I am getting an error message, when running the transcriptDB command from
> UCSC
>
> dm3KG<- makeTranscriptDbFromUCSC(genome="dm3",
> tablename="knownGene")Error in tableNames(ucscTableQuery(session,
> track = track)) :
>    error in evaluating the argument 'object' in selecting a method for
> function 'tableNames': Error in normArgTrack(track, trackids) :
> Unknown track: UCSC Genes
>
> I checked the tables supported by UCSC, The table is there:
>
>> supportedUCSCtables()                                 track           subtrack
> knownGene                   UCSC Genes<NA>
> knownGeneOld3           Old UCSC Genes<NA>
> wgEncodeGencodeManualV3  Gencode Genes    Genecode Manual

Not all the supported tables/tracks are available for all organisms.
UCSC only provides the "UCSC Genes" track for Human, Rat and Mouse.
For Fly you can either use the refGene table ("RefSeq Genes" track)
or the enGene table ("Ensembl Genes" track). See here for all the
tracks available for Fly at UCSC:

 
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=insect&org=D.+melanogaster&db=dm3&position=chr2L%3A826%2C001-851%2C000&hgt.suggest=&hgt.suggestTrack=refGene&pix=800&Submit=submit&hgsid=204682653

>
>
> Doing the same with the ensembl table works perfectly fine.

With makeTranscriptDbFromBiomart() you get the Ensembl genes, not
the UCSC genes.

Cheers,
H.

>
> Does anyone has an Idea as to why this is happening?
>
> Thanks
> Assa
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
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