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 -- Gowthaman Bioinformatics Systems Programmer. SBRI, 307 West lake Ave N Suite 500 Seattle, WA. 98109-5219 Phone : LAB 206-256-7188 (direct). [[alternative HTML version deleted]]

Hi Gowthaman, In GenomicFeatures in the development branch there is makeTranscriptDbFromGFF(). This man page describes how to use the Bioconductor development packages, library(BiocInstaller) ?useDevel Let us know if you have problems. Valerie 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 > >