cufflinks:single exon transcripts have no gene_id

[klebsiella]

Dear all,

In Cufflinks output, I noticed transcripts with no gene_id ' gene_id ""; '

Do you know what causes that and if this should be corrected and how ?

Best

[TiborNagy]

Maybe you run cufflinks without annotation.

[klebsiella]

No I precised the annotation file. Transcripts with more than one exons have a gene ID assigned to them. The problem is for single exon genes.

I can use gffread to purify the gff/gtf file from single exon genes.