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.
> >
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>
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