[BioC] how to make transcript db from ucsc for mm8

[Ou, Jianhong]

Dear Herve,

Great. Thanks a lot for your work.

Yours sincerely,

Jianhong Ou

LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605




On 11/16/13 6:51 AM, "Hervé Pagès" <hpages at fhcrc.org> wrote:

>Hi Jianhong,
>
>Thanks for the report. Problem came from the fact that
>makeTranscriptDbFromUCSC() was assuming that the "knownGene" table
>was always associated with the "UCSC Genes" track but this appears to
>not be true for old Human/Mouse/Rat assemblies where the track is
>called "Known Genes".
>
>This is fixed in GenomicFeatures 1.14.1 (release) and 1.15.3
>(devel). Both should become available via biocLite() in the
>next 30 hours or so.
>
>Cheers,
>H.
>
>
>On 11/13/2013 01:46 PM, Ou, Jianhong wrote:
>> Hi,
>>
>> I got error when I make transcript db from ucsc for mm8. Could anybody
>>help me to figure out this? Thanks in advance.
>>
>> 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
>>
>> The codes:
>> Library(GenomicFeatures)
>> mm8KG <- makeTranscriptDbFromUCSC(genome="mm8", tablename="knownGene")
>>
>> sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>>  base
>>
>> other attached packages:
>> [1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0   Biobase_2.22.0
>> rtracklayer_1.22.0     GenomicRanges_1.14.3   XVector_0.2.0
>>IRanges_1.20.5
>> [8] BiocGenerics_0.8.0
>>
>> loaded via a namespace (and not attached):
>>   [1] biomaRt_2.18.0    Biostrings_2.30.0 bitops_1.0-6
>>BSgenome_1.30.0   DBI_0.2-7         RCurl_1.95-4.1    Rsamtools_1.14.1
>>RSQLite_0.11.4    stats4_3.0.2
>> [10] tools_3.0.2       XML_3.95-0.2      zlibbioc_1.8.0
>>
>> Yours sincerely,
>>
>> Jianhong Ou
>>
>> LRB 670A
>> Program in Gene Function and Expression
>> 364 Plantation Street Worcester,
>> MA 01605
>>
>> 	[[alternative HTML version deleted]]
>>
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>
>-- 
>Hervé Pagès
>
>Program in Computational Biology
>Division of Public Health Sciences
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N, M1-B514
>P.O. Box 19024
>Seattle, WA 98109-1024
>
>E-mail: hpages at fhcrc.org
>Phone:  (206) 667-5791
>Fax:    (206) 667-1319