Converting GFF to GTF

Question

[Morgan]

Hello,

I am having trouble transferring my gff file to a gtf. I have tried using gffread, gffcompare, and rtracklayer, which all have left me with the same or no output. Here are my files. Please help!

• converted GTF
• original GFF

[Ram]

We're not going to download your files. Create a reproducible example and show us the commands you're running. If this is specific to Galaxy and does not involve command line invocation of tools, open a post in https://help.galaxyproject.org/ and delete this post.

[Morgan]

library(rtracklayer)
Orf50 <- system.file("Orf50.gff", package = "rtracklayer")
test_gff3 <- file.path(Orf50, "Orf50.gff")
test <- import(test_gff3)
export(test,"Orf50.gtf","gtf")

[Juke34]

Try AGAT

Answer 1

[Paul]

Run the following command, replacing input.gff with the name of your GFF file and output.gtf with the desired name for your GTF file:

gffread input.gff -T -o output.gtf

The -T option tells gffread to convert the input GFF file to GTF format.