[BioC] RNA-seq pathway analysis in Canis familiaris

[Jessica Perry Hekman]

Jim -- well, that code executed just fine, so now I'm moving forward 
with using the resulting object and seeing if it works for me. Thanks so 
much! I didn't expect just one line of code to solve my problem.

Jessica

On 5/16/14 12:58 PM, James W. MacDonald wrote:
> 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
>>
>>
>

-- 
Jessica P. Hekman, DVM, MS
PhD student, University of Illinois, Urbana-Champaign
Animal Sciences / Genetics, Genomics, and Bioinformatics