I try to convert the hg19_refGene.gtf file to a gff file with DEXseq_prepare_annotation.py. It doesn't work : my output file is empty. In DEXSeq's vignette they say that the script is made to be used with ensembl.gtf file. However I have conducted a full analysis at the gene level with the refGene.gtf file and I don't want to restart with a new mapping made on ensembl.gtf.

Is there any way to use refGene.gtf file with DEXseq_prepare_annotation.py ?

Many thanks