[BioC] RNA-seq pathway analysis in Canis familiaris

[James W. MacDonald]

Hi Jessica,

You have to build your own transcript package. Probably the easiest 
thing to do is

library(GenomicFeatures)
txdb.canFam3 <- makeTranscriptDbFromUCSC("canFam3","refGene")

Best,

Jim


On 5/16/2014 12:31 PM, Jessica Perry Hekman wrote:
> Hi, all. I am new to Bioconductor. I've tried hard to find the answer 
> to my question in online documentation, so I apologize if I'm asking 
> something which is already out there.
>
> I'm hoping to perform RNA-seq pathway analysis using GAGE and Pahview. 
> The RNAseq workflow documentation here:
>
> http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf 
>
>
> shows that a known-genes annotation package is required for this 
> workflow. The example uses human, TxDb.Hsapiens.UCSC.hg19.knownGene. 
> Some other species have pre-built packages, but not dog.
>
> I'm having trouble figuring out how to construct the equivalent 
> package for Canis familiaris 3.1. This vignette
>
> http://www.bioconductor.org/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf 
>
>
> (section 3) suggests that I can load a sqlite file based on UCSC known 
> gene data. I can't quite figure out how to construct this sqlite file. 
> Alternatively, I could load an annotation package such as 
> TxDb.Hsapiens.UCSC.hg19.knownGene, and I'd be willing to build one of 
> those for dog, but am not sure how.
>
> Any advice or pointers to appropriate documentation would be hugely 
> appreciated.
>
> Thanks,
> Jessica
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099