I decided to compare exon counts (DEXseq) and gene counts (HTSeq-count) for my alignments (done by STAR). Annotation(gtf) for mapping is just the same as that for counting. .gtf for DEXseq (modified by dexseq_prepare_annotation.py) a correspond to .gtf for HTSeq.
So everything seems ok, but I cannot interpret inconsistencies results. Under my hypothesis total count of exons should be somehow correlated with gene count. But what I see:
Why it is too small for ENSG00000000003 in HTSeq-count?
Thank you for answers,