[BioC] converting transcripts to gene level

[Valerie Obenchain]

You may want to check out the cummeRbund package. It doesn't do the 
conversion you want in but offers other storage and manipulation options 
of Cufflinks data that may be of interest. It's written by the authors 
of TopHat and Cufflinks.

Valerie


On 02/02/2012 04:42 AM, Michael Lawrence wrote:
> 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 at 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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