RNA-seq pathway analysis in Canis familiaris
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@jessica-perry-hekman-6556
Last seen 6.5 years ago
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/GenomicFea tures/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
RNASeq Genetics Annotation Canis familiaris gage RNASeq Genetics Annotation gage • 640 views
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@james-w-macdonald-5106
Last seen 12 hours ago
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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/GenomicF eatures/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
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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/Genomic Features/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
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