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 ).