Sbicolor_255_v2.1.gene_exons.gff3 to Sbicolor_255_v2.1.gene_exons.gtf conversion

Question

[sandeepmarla]

Hello All,

I have trouble converting Sbicolor_255_v2.1.gene_exons.gff3 file to Sbicolor_255_v2.1.gene_exons.gtf. I have used gffread of cufflinks to do the conversion. During the conversion process, gffread changed all the genes to exons (example is listed below). As a result, HTSeq couldn't count the transcripts as the gene information is missing. Please suggest a best way to fix this problem.

Sbicolor_255_v2.1.gene_exons.gff3

Chr01    phytozomev10    gene    1619    2809    .    +    .    ID=Sobic.001G000100.v2.1;Name=Sobic.001G000100
Chr01    phytozomev10    mRNA    1619    2809    .    +    .    ID=Sobic.001G000100.1.v2.1;Name=Sobic.001G000100.1;pacid=28395113;longest=1;Parent=Sobic.001G000100.v2.1

Sbicolor_255_v2.1.gene_exons.gtf

Chr01    phytozomev10    exon    1619    2809    .    +    .    transcript_id "Sobic.001G000100.1.v2.1"; gene_id "Sobic.001G000100.v2.1"; gene_name "Sobic.001G000100";
Chr01    phytozomev10    CDS    1951    2616    .    +    0    transcript_id "Sobic.001G000100.1.v2.1"; gene_id "Sobic.001G000100.v2.1"; gene_name "Sobic.001G000100";

Thanks