Question: Conversion Of Grangeslist To Gff File
gravatar for Milica
8.8 years ago by
Milica0 wrote:


I work with the RNA Seq data from F.catus (cat). I need a GFF file. Does anyone know a way or already existing method how to produce such a file. I can read into R a GRangesList object from Biomart which contains annotated cat genes. Is there a way to convert GRangesList object to a GFF file?

Thank you!

R gff conversion • 4.8k views
ADD COMMENTlink modified 8.8 years ago by Sukhi Singh10k • written 8.8 years ago by Milica0

have you looked at the granges reference and gff format spec? and ? it seems like most people do their processing within R so they are mostly looking to import gff instead of export if you want the annotations you might want to check out or

ADD REPLYlink modified 15 months ago by _r_am32k • written 8.8 years ago by Ying W4.0k
gravatar for Sukhi Singh
8.8 years ago by
Sukhi Singh10k
Sukhi Singh10k wrote:

I think you need rtracklayer and check the function export.gff. This package works with Granges which you already have and you can export to a variety of formats. I used it to export GRanges to a bed file. Also Check this question.


ADD COMMENTlink written 8.8 years ago by Sukhi Singh10k
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