Any tools to convert .gff to .gtf format
2
0
Entering edit mode
@66ce6032
Last seen 19 months ago
India

Im beginner in R and I want to convert my casuarina_genome.gff file to casuarina_genome.gtf. After looking for several web links I couldn't convert it to .gtf. The purpose of .gtf extension is to provide the genome.gtf file into crispRdesignR package to check for off-targets. Kindly help me out to convert the .gff to .gtf.

AnnotationData CrispRdesignR BSgenome • 5.1k views
ADD COMMENT
0
Entering edit mode
Guido Hooiveld ★ 3.9k
@guido-hooiveld-2020
Last seen 16 hours ago
Wageningen University, Wageningen, the …

Maybe this overview helps: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gff_to_gtf.md

You might also be able to use the Bioconductor package rtracklayer for this:

library(rtracklayer)

test_path <- system.file("tests", package = "rtracklayer")
test_gff3 <- file.path(test_path, "genes.gff3")
test <- import(test_gff3)
export(test,"test.gtf","gtf")

Code is from a post at Biostars I once saw.

ADD COMMENT
0
Entering edit mode
Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 7 days ago
United States

The gffread utility can convert from gff to gtf quite nicely and is generally useful for other processing on gff files (extracting fast of genes, etc).

ADD COMMENT

Login before adding your answer.

Traffic: 905 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6