I'm attempting to use htseq-count to get read counts for some *Plasmodium *RNA-seq data. The command line looks as follows:
htseq-count --format=bam --order=pos 3D7_1-1.bam PlasmoDB-28_Pfalciparum3D7.gff
However, when I run the command I get the following error:
Error occured when processing GFF file (line 40 of file PlasmoDB-28_Pfalciparum3D7.gff): Feature exon_PF3D7_0100100-1 does not contain a 'gene_id' attribute [Exception type: ValueError, raised in count.py:53]
Is there a way to tell htseq-count to ignore any features that don't have a 'gene_id' attribute or a way to convert the gff I have to a gtf? Any ideas/help much appreciated.