How can I use RefGene.gtf with DEXSeq

[jisdb]

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

[dpryan]

Does it give you an error? As I recall, refGene has the unfortunate property of having duplicate identifiers on multiple chromosomes/strands...which completely breaks any script trying to prepare inputs for DEXSeq.

Rule of thumb: Always use Ensembl and never UCSC.

[jisdb]

It doesn't give an error but the gff file is empty. So, I can't use DEXSeq with refGene ?

[dpryan]

You might need to munge the GTF file a bit. Play around with the python script to see why it's giving an empty output. The fix might end up being simple.