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Wrong naming of transcript in gtf/gff3

Hi all,

Can someone tell me why naming transcript_id "jg1.t1"; gene_id "jg1"; at a gtf is not proper GFF file?

Thanks in advance

format gtf gff3
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updated by Juke34 Juke34 • written by Diego • Diego

Hi,

Softwares/packages such as EvidenceModeler, Augustus, and gff3tolkit always says that the ID is wrong.

CAKLNU010000942.1   other_pred1 CDS 724 1083    0.38    +   0   transcript_id "jg1.t1"; gene_id "jg1";
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Diego • Diego

This is a CDS, is there a transcript with transcript_id "jg1.t1" and/or a gene with gene_id "jg1" in the very same file ?

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written by Pierre Lindenbaum Pierre Lindenbaum

yes. The gtf look like this

CAEGAH010020538.1      AUGUSTUS       transcript     407    7407   0.08   -      .      transcript_id "g1.t1"; gene_id "g1";
CAEGAH010020538.1      AUGUSTUS       exon   407    547    .      -      .      transcript_id "g1.t1"; gene_id "g1";
CAEGAH010020538.1      AUGUSTUS       exon   6202   7407   .      -      .      transcript_id "g1.t1"; gene_id "g1";
CAEGAH010020538.1      AUGUSTUS       CDS    407    547    .      -      0      transcript_id "g1.t1"; gene_id "g1";
CAEGAH010020538.1      AUGUSTUS       CDS    6202   7407   .      -      0      transcript_id "g1.t1"; gene_id "g1";
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Diego • Diego

or like this one I have converted it into gff3:

CAKLNU010000942.1       gffcl   locus   724     2835    .       +       .       ID=RLOC_00000001;transcripts=jg1.t1
CAKLNU010000942.1       AUGUSTUS        transcript      724     2835    .       +       .       ID=jg1.t1;geneID=jg1;locus=RLOC_00000001
CAKLNU010000942.1       AUGUSTUS        CDS     724     1083    .       +       0       Parent=jg1.t1
CAKLNU010000942.1       AUGUSTUS        CDS     1181    1625    0.34    +       0       Parent=jg1.t1
CAKLNU010000942.1       AUGUSTUS        CDS     2270    2835    0.42    +       2       Parent=jg1.t1
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Diego • Diego

1 answer

GFF formats require ID attributes for features (gene, transcript, exon, etc.) while in GTF you must have gene_id for all features and ?transcript_id for all features excepted gene feature. For more details of differences between the two format, you can read this: https://agat.readthedocs.io/en/latest/gxf.html

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written by Juke34 Juke34

thanks for the very useful reply. I wonder why most tools are gff2gtf and not in the other way around. I guess these tools can do gft2gff as well. I am going to check agat

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written by Diego • Diego

I think this is what I looking for: agat_convert_sp_gxf2gxf.pl

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written by Diego • Diego

can agat_sp_ensembl_output_style.pl do this: -g non-ensembl.gtf [ -o ensembl_like.gtf ] ?

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written by Diego • Diego

Potentially yes but you have to use AGAT >=1.0.0 and modify the AGAT config to specify that you want GTF output.

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written by Juke34 Juke34

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