converting transcripts to gene level
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@abhishek-pratap-5083
Last seen 7.1 years ago
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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@michael-lawrence-3846
Last seen 13 days ago
United States
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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