Using GTF gene annotation to build a GemomicRanges Object
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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.
RNASeq Annotation RNASeq Annotation • 1.9k views
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@vincent-j-carey-jr-4
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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]]
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Sunny Yu Liu ▴ 80
@sunny-yu-liu-4982
Last seen 7.0 years ago
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]]
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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]]
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Sunny Yu Liu ▴ 80
@sunny-yu-liu-4982
Last seen 7.0 years ago
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]]
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