Question: Convertion Of Gff3 To Gtf
12
gravatar for geek_y
6.4 years ago by
geek_y8.7k
geek_y8.7k wrote:

How do I convert GFF file to a GTF file? Is there any tool available ?    

gff gtf • 42k views
ADD COMMENTlink modified 5 months ago by Asbesto0 • written 6.4 years ago by geek_y8.7k

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

ADD REPLYlink written 6.4 years ago by Ying W3.8k
25
gravatar for gleparc
4.8 years ago by
gleparc250
gleparc250 wrote:

The easiest way is to use the gffread program that comes with the Cufflinks software suite (Tuxedo)

gffread my.gff3 -T -o my.gtf

See gffread -h for more information

ADD COMMENTlink written 4.8 years ago by gleparc250

This should be an answer! It worked for me, thanks.

ADD REPLYlink written 3.6 years ago by SES8.1k

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.

ADD REPLYlink written 14 months ago by boczniak767610
7
gravatar for Paolo
6.4 years ago by
Paolo220
Trieste
Paolo220 wrote:

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")
ADD COMMENTlink written 6.4 years ago by Paolo220

It helped. Thanks :)

ADD REPLYlink written 18 months ago by sangram_keshari50

I'm not sure if this produce really gtf, after above commands I have "gff-version 2" in the header of exported file.

ADD REPLYlink written 14 months ago by boczniak767610
1

The GTF (General Transfer Format) is identical to GFF version 2. https://uswest.ensembl.org/info/website/upload/gff.html

ADD REPLYlink written 10 months ago by bhanratt10
1
gravatar for Arun
6.4 years ago by
Arun2.3k
Germany
Arun2.3k wrote:

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:

The whole point of the GTF format was to standardise certain aspects that are left open in GFF. Hence, there are many different valid ways to encode the same information in a valid GFF format, and any parser or converter needs to be written specifically for the choices the author of the GFF file made. For example, a GTF file requires the gene ID attribute to be called "gene_id", while in GFF files, it may be "ID", "Gene", something different, or completely missing. Hence, a general GFF-to-GTF converter (as opposed to one converting only GFF files from a very specific source) needs to guess this from the data, which is non-trivial.

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.

ADD COMMENTlink written 6.4 years ago by Arun2.3k
0
gravatar for Asbesto
5 months ago by
Asbesto0
Asbesto0 wrote:

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?

ADD COMMENTlink written 5 months ago by Asbesto0
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