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gowtham | 3 Aug 2012 00:38
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creating transcriptDB from gff3 files

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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-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).

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Valerie Obenchain | 3 Aug 2012 02:12

Re: creating transcriptDB from gff3 files

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
>
>

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