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:
ENSG00000000003:001 248 ENSG00000000003:002 86 ENSG00000000003:003 63 ENSG00000000003:004 56 ENSG00000000003:005 66 ENSG00000000003:006 105 ENSG00000000003:007 91 ENSG00000000003:008 82 ENSG00000000003:009 80 ENSG00000000003:010 0 ENSG00000000003:011 16 ENSG00000000003:012 5 ENSG00000000003:013 0 ENSG00000000003:014 1 ENSG00000000003:015 2 ENSG00000000005:001 0 ENSG00000000005:002 0 ENSG00000000005:003 0 ENSG00000000005:004 0 ENSG00000000005:005 0 ENSG00000000005:006 0 ENSG00000000005:007 0 ENSG00000000005:008 0 ENSG00000000005:009 2
ENSG00000000003 2 ENSG00000000005 2
Why it is too small for ENSG00000000003 in HTSeq-count?
Thank you for answers,