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gff to gtf missing gene id

Hi,

I was trying my hand at annotating a genome using prokka, and I've converted the output gff file to gtf (gffread file.gff -T -o file.gtf) and this is what my gtf file looks like:

CP001095.1  prokka  transcript  210 1712    .   +   .   transcript_id "LCLPEOGO_00001_gene"; gene_id "LCLPEOGO_00001_gene"; gene_name "dnaA"
CP001095.1  prokka  CDS 210 1712    .   +   0   transcript_id "LCLPEOGO_00001_gene"; gene_name "dnaA";
CP001095.1  prokka  transcript  2447    3571    .   +   .   transcript_id "LCLPEOGO_00002_gene"; gene_id "LCLPEOGO_00002_gene"; gene_name "dnaN_1"
CP001095.1  prokka  CDS 2447    3571    .   +   0   transcript_id "LCLPEOGO_00002_gene"; gene_name "dnaN_1";

Every second line is missing the gene id, the gtf file format descriptions online look different to mine, is there something wrong with my output? or can I continue to work with this - I would really like to make use of it in FeatureCounts (sorry in advance if this is a really noob question. Any help is appreciated xx ).

transcriptomics annotation
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updated by Ram Ram • written by plain_text • plain_text

Thanks for the suggestion, if nothing else works I'll just specify for the cds and see what happens :)

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written by plain_text • plain_text

1 answer

You can fix that using AGAT:

agat_convert_sp_gff2gtf.pl --gff test.gtf 

##gtf-version 3
CP001095.1  prokka  gene    210 1712    .   +   .   gene_id "LCLPEOGO_00001_gene"; transcript_id "LCLPEOGO_00001_gene"; ID "nbisL1-gene-1"; gene_name "dnaA";
CP001095.1  prokka  transcript  210 1712    .   +   .   gene_id "LCLPEOGO_00001_gene"; transcript_id "LCLPEOGO_00001_gene"; ID "LCLPEOGO_00001_gene"; Parent "nbisL1-gene-1"; gene_name "dnaA";
CP001095.1  prokka  exon    210 1712    .   +   .   gene_id "LCLPEOGO_00001_gene"; transcript_id "LCLPEOGO_00001_gene"; ID "nbis-exon-1"; Parent "LCLPEOGO_00001_gene"; gene_name "dnaA";
CP001095.1  prokka  CDS 210 1712    .   +   0   gene_id "LCLPEOGO_00001_gene"; transcript_id "LCLPEOGO_00001_gene"; ID "cds-1"; Parent "LCLPEOGO_00001_gene"; gene_name "dnaA";
CP001095.1  prokka  gene    2447    3571    .   +   .   gene_id "LCLPEOGO_00002_gene"; transcript_id "LCLPEOGO_00002_gene"; ID "nbisL1-gene-2"; gene_name "dnaN_1";
CP001095.1  prokka  transcript  2447    3571    .   +   .   gene_id "LCLPEOGO_00002_gene"; transcript_id "LCLPEOGO_00002_gene"; ID "LCLPEOGO_00002_gene"; Parent "nbisL1-gene-2"; gene_name "dnaN_1";
CP001095.1  prokka  exon    2447    3571    .   +   .   gene_id "LCLPEOGO_00002_gene"; transcript_id "LCLPEOGO_00002_gene"; ID "nbis-exon-2"; Parent "LCLPEOGO_00002_gene"; gene_name "dnaN_1";
CP001095.1  prokka  CDS 2447    3571    .   +   0   gene_id "LCLPEOGO_00002_gene"; transcript_id "LCLPEOGO_00002_gene"; ID "cds-2"; Parent "LCLPEOGO_00002_gene"; gene_name "dnaN_1";
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written by Juke34 Juke34

Haven't looked at AGAT before, will try that, thanks!

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written by plain_text • plain_text

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