Hi there,

I am having problem with the DEXseq package.

I want to test if the exon usage of honey bee (Apis mellifera) has changed after infection.

As the DEXseq package suggests, I downloaded the honey bee genome fasta file and the annotation gff file from ensembl website, but I cannot find the gtf file from ensembl. 

Thus, it seems I cannot create the annotation file which specific use for the DEXseq package and I tried the gtf file from the NCBI by using dexseq_prepare_annotation.py script.

However, after create the DEXseq annotation gff file, I use dexseq_count.py to count the reads.

ALL the reads are in the ambiguous_readpair_position and empty categories.

I tried different combinations of the annotation file and the genome fasta, still the same thing happened.

Can somebody give me some tips on this ? 

Thank you in advance!!!