Hi,

There's nothing that does exactly that. You can use
rtracklayer::import(gtf, format = "gff2") to get the file into a RangedData
or GRanges. And then after your manipulations write it out again with
export(object, file, "gff2").

Michael

On Wed, Feb 1, 2012 at 5:15 PM, Abhishek Pratap <apratap@lbl.gov> wrote:

> Hi All
>
> I have cufflinks generated transcripts file in gtf format. I wondering
> if I can use any R package to convert it to gene level gtf file. By
> this means all the transcripts are collapsed into genes and each gene
> contains all the exons seen in all the transcripts for that gene.
>
>
> Sample Data attached.
>
> In the attached GTF file I have 3 made up transcripts from 2 genes.
> What I would want to get as a output is a gtf file containing two
> genes and all the exons associated with them.
>
> Thanks!
> -Abhi
>
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