My annotation file is in .gff format. I would like to convert it to .gtf format or to know if there is a way to directly download the annotation file in .gtf format?
I am working on sequences from the P Falicparum 3D7.
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$\begingroup$ I think the question was already extensively answered here: bioinformatics.stackexchange.com/questions/2068/… $\endgroup$– aechchikiJan 31, 2020 at 10:06
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$\begingroup$ Thank you for your awnser $\endgroup$– DiangoFeb 1, 2020 at 6:21
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4 Answers
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You can use gffread to convert gff to gtf2, below is from the manual:
In order to see the GTF2 version of the same transcripts, the -T option should be added:
gffread -E annotation.gff -T -o- | moreThe examples above also show that gffread can be used to convert a file between GTF2 and GFF3 file formats.
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I would suggest to use agat_convert_sp_gff2gtf.pl from AGAT because you loose information with gffread.
e.g here a gff example:
##gff-version 3
scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2
scaffold625 maker transcript 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458
scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker exon 337818 337971 . + 0 ID=CLUHART00000008717:exon1;Parent=CLUHART00000008717
scaffold625 maker exon 340733 340841 . + 0 ID=CLUHART00000008717:exon2;Parent=CLUHART00000008717
scaffold625 maker exon 341518 341628 . + 2 ID=CLUHART00000008717:exon3;Parent=CLUHART00000008717
scaffold625 maker exon 341964 343277 . + 2 ID=CLUHART00000008717:exon4;Parent=CLUHART00000008717
scaffold625 maker five_prime_UTR 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
with gffread you get:
scaffold625 maker transcript 337818 343277 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker exon 337818 337971 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker exon 340733 340841 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker exon 341518 341628 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker exon 341964 343277 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker CDS 337915 337971 . + 0 transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker CDS 340733 340841 . + 0 transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker CDS 341518 341628 . + 2 transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker CDS 341964 343033 . + 2 transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
while with AGAT you get
scaffold625 maker gene 337818 343277 . + . ID CLUHARG00000005458 ; Name TUBB3_2 ; gene_id CLUHARG00000005458
scaffold625 maker mRNA 337818 343277 . + . ID CLUHART00000008717 ; Parent CLUHARG00000005458 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker exon 337818 337971 . + 0 ID "CLUHART00000008717:exon1" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker exon 340733 340841 . + 0 ID "CLUHART00000008717:exon2" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker exon 341518 341628 . + 2 ID "CLUHART00000008717:exon3" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker exon 341964 343277 . + 2 ID "CLUHART00000008717:exon4" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker CDS 337915 337971 . + 0 ID "CLUHART00000008717:cds" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker CDS 340733 340841 . + 0 ID "CLUHART00000008717:cds" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker CDS 341518 341628 . + 2 ID "CLUHART00000008717:cds" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker CDS 341964 343033 . + 2 ID "CLUHART00000008717:cds" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker five_prime_UTR 337818 337914 . + . ID "CLUHART00000008717:five_prime_utr" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
scaffold625 maker three_prime_UTR 343034 343277 . + . ID "CLUHART00000008717:three_prime_utr" ; Parent CLUHART00000008717 ; gene_id CLUHARG00000005458 ; transcript_id CLUHART00000008717
So you can see as example that Name=TUBB3_2 from the gene feature disappeared with gffread.
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Actually I started a mini-review about the tools to do such conversion.
You can find it here:
https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gff_to_gtf.md
As I mentioned earlier they do not behave all the same way...
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You can try bioinfokit (https://github.com/reneshbedre/bioinfokit) in python.
from bioinfokit.analys import gff
gff.gff_to_gtf(file="yourfile.gff3")
# The converted gtf file will be saved in the same working directory.
```
