Intron feature missing in the gtf

[xyz0o]

my gff file has intron annotations but they disappear in the gtf. I tried different versions of gtf but they don't work for me and only the standard default version creates an output and that does not include introns. How can I add them into the gtf file?

my code is agat_convert_sp_gff2gtf.pl --gff <filename> -o <filename>

[Juke34]

could you provide a piece of sample to test? What AGAT version are you using?

[Juke34]

I have tested with that file and it works perfectly well

[xyz0o]

I had this file:

4_chromosome_RagTag Liftoff gene    3158047 3176805 .   -   .   ID=g11135;coverage=1.0;sequence_ID=0.997;valid_ORFs=0;extra_copy_number=0;copy_num_ID=g11135_0
4_chromosome_RagTag Liftoff mRNA    3158047 3176805 .   -   .   ID=g11135.t1;Parent=g11135;matches_ref_protein=True;valid_ORF=False;missing_stop_codon=True;extra_copy_number=0
4_chromosome_RagTag .   intron  3160656 3167831 .   -   .   Parent=g11135.t1

and the result is:

4_chromosome_RagTag Liftoff gene    3160656 3167831 .   -   .   gene_id "g11135"; ID "g11135"; copy_num_ID "g11135_0"; coverage "1.0"; extra_copy_number "0"; sequence_ID "0.997"; valid_ORFs "0";
4_chromosome_RagTag Liftoff transcript  3160656 3167831 .   -   .   gene_id "g11135"; transcript_id "g11135.t1"; ID "g11135.t1"; Parent "g11135"; extra_copy_number "0"; matches_ref_protein "True"; missing_stop_codon "True"; original_biotype "mrna"; valid_ORF "False";

I am using the singularity container and have just downloaded it yesterday so it should be the latest version: agat_1.0.0--pl5321hdfd78af_0.sif

`

[Juke34]

Oh right you are using version 1.0.0. So then you fall in a particular bug that has been fixed in most recent versions. Please use v1.4.0.

[xyz0o]

Oh I see, I got it form the main page so it was not updated to the latest version :) https://github.com/NBISweden/AGAT?tab=readme-ov-file#install-agat

Thanks, I will check that

[xyz0o]

using the latest version solved my problem, thanks.