[BioC] creating transcriptDB from gff3 files

Valerie Obenchain vobencha at fhcrc.org
Fri Aug 3 02:12:30 CEST 2012

Hi Gowthaman,

In GenomicFeatures in the development branch there is 
makeTranscriptDbFromGFF(). This man page describes how to use the 
Bioconductor development packages,


Let us know if you have problems.


On 08/02/12 15:38, gowtham wrote:
> Hi Everyone,
> I am wondering if there is a tool to create transcriptDB object from gff3
> file. GenomicFeatures package does not seem to have a method to create it
> from GFF. (we work with non model organisms, so no ucsc/biomart available
> for us).
> I should be able to create it with  'makeTranscriptDb(transcripts,
> splicings, genes=NULL, chrominfo=NULL, metadata=NULL, ...)', but wondering
> if there is any tool that already does this?
> Thanks verymuch in advance,
> Gowthaman

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