

Hi
Marc,

 

Sorry
to hijack the topic. I just wonder if there is any way to create a transcriptDb
object using a TCGA GAF file (

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/other/GAF/GAF_bundle/outputs/TCGA.Sept2010.09202010.gaf)

)?

 

I looked at the devel version of
GenomicFeatures package and cannot find any information.

 

Thanks a lot,

 

Ying

> Date: Tue, 18 Sep 2012 09:16:06 -0700
> From: mcarlson@fhcrc.org
> To: bioconductor@r-project.org
> Subject: Re: [BioC] Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer
> 
> Hi Joachim,
> 
> The version of the GenomicFeatures package in the development branch of 
> Bioconductor has had this functionality since the spring.  The new 
> release scheduled for October 2nd will also have it.
> 
> 
>    Marc
> 
> 
> 
> On 09/18/2012 08:36 AM, Bargsten, Joachim wrote:
> > Hi all,
> > I tried to figure out how to get GFF3 annotation data into a
> > TranscriptDb object. So far, I could only find the posts in this thread
> > and the proposed solution did not work very well for me. In the end, I
> > implemented a "makeTranscriptDbFromGFF3" function myself. For those who
> > are interested, you can find my version on:
> >
> > https://gist.github.com/3743732
> >
> >
> > 	Joachim
> > _______________________________________________
> > 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
> 
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