How do I convert GFF file to a GTF file? Is there any tool available?
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written
by
GouthamAtla
3 answers
gffread from Cufflinks version 2.2.1 not work properly, it leaves only "gene_id" and "transcript_id" from the 9th column. E.g. exon number was stripped. I've not used the latest version, because I couldn't find the binaries and don't want to install additional packages needed for compilation.
Worked for me.Thank you so much.
Take a look at the rtracklayer Bioconducor package:
?import.gff3
test_path <- system.file("tests", package = "rtracklayer")
test_gff3 <- file.path(test_path, "genes.gff3")
test <- import(test_gff3)
export(test,"test.gtf","gtf")
It helped. Thanks :)
I'm not sure if this produce really gtf, after above commands I have "gff-version 2" in the header of exported file.
The GTF (General Transfer Format) is identical to GFF version 2. https://uswest.ensembl.org/info/website/upload/gff.html
Thanks AGAT works well.
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It would help to know what your downstream analysis/usage is? If GTF is an intermediate step towards another conversion, I suggest you try to obtain directly the final format. From seqanswers:
In general, it is difficult to get this right unless you are working on 1 particular GFF file as GFF is more general than GTF.
in gerneral, gtf is a subset of gff that is used often for counting peaks in RNA-seq data, it would be very useful if you gave more information on what you are trying to do. You can find the specifications for GFF3 here: http://www.sequenceontology.org/gff3.shtml GTF http://mblab.wustl.edu/GTF22.html and GFF http://www.sanger.ac.uk/resources/software/gff/spec.html
Hi,
I'm still looking for a tool that allow to make a conversion from GenBank data to gtf for species that are not in ENSEMBL database. Any suggestions?