Any tools to convert .gff to .gtf format
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@66ce6032
Last seen 22 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 • 5.9k views
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Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 13 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.

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Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 10 weeks 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).

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appsierra8 • 0
@eee6f0de
Last seen 10 days ago
India

Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. Appsierra is providing the best software testing services and development company, known for delivering high-quality tools and services. You can check out their website for more information and to access the tool.

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