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Question: Using GTF gene annotation to build a GemomicRanges Object
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6.0 years ago by
Guest User12k
Guest User12k wrote:
Any R based package to integrate GTF format gene annotation to GenomicRanges object? or make a .sqlite object then can be saved (saveFeatures) for future use? really need this tool for RNAseq data analysis. Thank you very much! -- output of sessionInfo(): library(GenomicFeatures) library(Rsamtools) commands used: makeTranscriptsDbfromUCSC saveFeatures("ensGene.sqlite") loadFeatures("ensGene.sqlite") -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 6.0 years ago by Sunny Yu Liu80 • written 6.0 years ago by Guest User12k
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gravatar for Vincent J. Carey, Jr.
6.0 years ago by
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Vincent J. Carey, Jr.6.2k wrote:
did you try a google search with "bioconductor import GTF" -- there are a few direct solutions including http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Parsing-Gene- Intergenic-Regions-Bas On Tue, Nov 29, 2011 at 2:05 PM, sunny [guest] <guest@bioconductor.org>wrote: > > Any R based package to integrate GTF format gene annotation to > GenomicRanges object? or make a .sqlite object then can be saved > (saveFeatures) for future use? > really need this tool for RNAseq data analysis. Thank you very much! > > > > -- output of sessionInfo(): > > library(GenomicFeatures) > library(Rsamtools) > > commands used: makeTranscriptsDbfromUCSC > saveFeatures("ensGene.sqlite") > loadFeatures("ensGene.sqlite") > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by Vincent J. Carey, Jr.6.2k
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gravatar for Sunny Yu Liu
6.0 years ago by
Sunny Yu Liu80
Sunny Yu Liu80 wrote:
Thanks! I also have an idea to do it.... wish it works... -----Original Message----- From: Vincent Carey [mailto:stvjc@channing.harvard.edu] Sent: Tue 11/29/2011 3:49 PM To: sunny [guest] Cc: bioconductor@r-project.org; Sunny Yu Liu Subject: Re: [BioC] Using GTF gene annotation to build a GemomicRanges Object did you try a google search with "bioconductor import GTF" -- there are a few direct solutions including http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Parsing-Gene- Intergenic-Regions-Bas On Tue, Nov 29, 2011 at 2:05 PM, sunny [guest] <guest@bioconductor.org>wrote: > > Any R based package to integrate GTF format gene annotation to > GenomicRanges object? or make a .sqlite object then can be saved > (saveFeatures) for future use? > really need this tool for RNAseq data analysis. Thank you very much! > > > > -- output of sessionInfo(): > > library(GenomicFeatures) > library(Rsamtools) > > commands used: makeTranscriptsDbfromUCSC > saveFeatures("ensGene.sqlite") > loadFeatures("ensGene.sqlite") > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by Sunny Yu Liu80
The rtracklayer package can parse GTF, via import(). Then you just pass the resulting pieces to makeTranscriptDb(). That latter part is not so trivial though. I recently made the inverse for GFF3, i.e., outputting a TranscriptDb as GFF3 (see asGFF in devel rtracklayer/GenomicFeatures). I could imagine a direct importer of GFF3 and BED to TranscriptDb. Recent improvements to rtracklayer should make this easy. Any takers? Michael On Tue, Nov 29, 2011 at 1:14 PM, Sunny Yu Liu <sunny@lunenfeld.ca> wrote: > Thanks! > I also have an idea to do it.... wish it works... > > > > -----Original Message----- > From: Vincent Carey [mailto:stvjc@channing.harvard.edu] > Sent: Tue 11/29/2011 3:49 PM > To: sunny [guest] > Cc: bioconductor@r-project.org; Sunny Yu Liu > Subject: Re: [BioC] Using GTF gene annotation to build a GemomicRanges > Object > > did you try a google search with "bioconductor import GTF" -- there are a > few direct solutions including > > > http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Parsing-Gene- Intergenic-Regions-Bas > > > On Tue, Nov 29, 2011 at 2:05 PM, sunny [guest] <guest@bioconductor.org> >wrote: > > > > > Any R based package to integrate GTF format gene annotation to > > GenomicRanges object? or make a .sqlite object then can be saved > > (saveFeatures) for future use? > > really need this tool for RNAseq data analysis. Thank you very much! > > > > > > > > -- output of sessionInfo(): > > > > library(GenomicFeatures) > > library(Rsamtools) > > > > commands used: makeTranscriptsDbfromUCSC > > saveFeatures("ensGene.sqlite") > > loadFeatures("ensGene.sqlite") > > > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by Michael Lawrence9.8k
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gravatar for Sunny Yu Liu
6.0 years ago by
Sunny Yu Liu80
Sunny Yu Liu80 wrote:
worthy to have a try... thanks! -----Original Message----- From: Michael Lawrence [mailto:lawrence.michael@gene.com] Sent: Tue 11/29/2011 6:08 PM To: Sunny Yu Liu Cc: Vincent Carey; bioconductor@r-project.org Subject: Re: [BioC] Using GTF gene annotation to build a GemomicRanges Object The rtracklayer package can parse GTF, via import(). Then you just pass the resulting pieces to makeTranscriptDb(). That latter part is not so trivial though. I recently made the inverse for GFF3, i.e., outputting a TranscriptDb as GFF3 (see asGFF in devel rtracklayer/GenomicFeatures). I could imagine a direct importer of GFF3 and BED to TranscriptDb. Recent improvements to rtracklayer should make this easy. Any takers? Michael On Tue, Nov 29, 2011 at 1:14 PM, Sunny Yu Liu <sunny@lunenfeld.ca> wrote: > Thanks! > I also have an idea to do it.... wish it works... > > > > -----Original Message----- > From: Vincent Carey [mailto:stvjc@channing.harvard.edu] > Sent: Tue 11/29/2011 3:49 PM > To: sunny [guest] > Cc: bioconductor@r-project.org; Sunny Yu Liu > Subject: Re: [BioC] Using GTF gene annotation to build a GemomicRanges > Object > > did you try a google search with "bioconductor import GTF" -- there are a > few direct solutions including > > > http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Parsing-Gene- Intergenic-Regions-Bas > > > On Tue, Nov 29, 2011 at 2:05 PM, sunny [guest] <guest@bioconductor.org> >wrote: > > > > > Any R based package to integrate GTF format gene annotation to > > GenomicRanges object? or make a .sqlite object then can be saved > > (saveFeatures) for future use? > > really need this tool for RNAseq data analysis. Thank you very much! > > > > > > > > -- output of sessionInfo(): > > > > library(GenomicFeatures) > > library(Rsamtools) > > > > commands used: makeTranscriptsDbfromUCSC > > saveFeatures("ensGene.sqlite") > > loadFeatures("ensGene.sqlite") > > > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by Sunny Yu Liu80
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