Hello,

I'm trying to interpret the exon numbering in the third column of the table output from Dexseq, as well on Expression  plot.  I've used Dexseq-count followed by Dexseq on two replicates of human tumor vs normal RNA-Seq transcriptome data (hg19).

The first column shows multiple ENSG ids followed by the exon number.  Which id does the exon number corresponds to? 

Also, the number of exons is greater than it should be. For example: it groups ENSG000000251349, ENSG00000241697 and ENSG00000066697 and lists a total of 25 exons which is incorrect.  

Thank you for your help

Hi yelekley, I think the answers to these questions are in the section "2.4 Preparing the annotation" of the DEXSeq vignette. Did you already have a look at it? If something is unclear from this description please let us know and we will be happy to clarify it.