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

[Hervé Pagès]

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
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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