I have some analysis recently with DEXSeq package, on RNA-seq data (paired-end, mouse), following the very nicely written vignette and manual that are provided (including the DEXSeq Python scripts to build the counts matrix etc).
My issue though concerns the "Gene Model" that is drawn in the plots output. Although for many genes, this gene model corresponds indeed to the RefSeq given in UCSC or Ensembl, for many others, the gene model drawn on the top does not seem to make really sense.
At the beginning, I thought that this could be due to loci where there are multiple isoforms with different exons overlapping more or less etc, and that the Gene Model would thus correspond to a kind of "sum" of all the existing exons. But even like that, the exons of the Gene Model clearly don't "fit" to the exons of all the shown isoforms and transcripts on that region.
My question: how is the Gene Model built?
ps: since it does not seem that pictures can be inserted in the text directly, I can send some pictures by email. I have for instance a locus where it says that the Gene Model has something like 42 exons, while this is clearly not true (at least, from the RefSeq info). The exons E37, E38 and E39 of that locus (same for E26/E27/E28, or E31/E32) seem to fit only to introns or to a subsection of the last exon of a given isoform.