I'd like to run DEXseq on my RNA-seq dataset to identify any potential differences in exon inclusion between samples. I used HISAT2 to generate BAM files of aligned reads, and then DEXseq-Count mode-prepare to generate an annotation GFF file. My reference genome for alignments was hg38, and I used the ENSEMBL hg38 gene annotation GTF to prepare my GFF file. However, whenever I try to run DEXseq-Count in count mode, I obtain zero counts for all exons. I have separately run transcript-level analyses on these BAM files, so I know they're okay and I should be getting non-zero exon counts. Any ideas what I might be doing wrong?
Thanks for your help.