Question: Conversion Of Grangeslist To Gff File
0
gravatar for Milica
7.3 years ago by
Milica0
Milica0 wrote:

Hello!

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 • 4.0k views
ADD COMMENTlink modified 7.2 years ago by Sukhdeep Singh9.8k • written 7.3 years ago by Milica0

have you looked at the granges reference and gff format spec? http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html and http://www.sanger.ac.uk/resources/software/gff/spec.html ? 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 http://genome.ucsc.edu/cgi-bin/hgTables?command=start or http://uswest.ensembl.org/biomart/martview

ADD REPLYlink written 7.2 years ago by Ying W3.9k
0
gravatar for Sukhdeep Singh
7.2 years ago by
Sukhdeep Singh9.8k
Netherlands
Sukhdeep Singh9.8k 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.

Cheers

ADD COMMENTlink written 7.2 years ago by Sukhdeep Singh9.8k
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