Hi all! The total number of exon for the ZEB2 gene is greater than what has been reported in literature. DEXSeq shows 106 Exons since it should be 10. So im confused, how exactly does dexse_prepare_annotation.py prepares the file fpr further analysis? Since i have more exons than usual in my analysis, is there a way to tell which "additionally" exon is corresponding to the "real exon" i.e. Exon_Bin1-14 corresponds to Exon 1 from the ZEB2 gene Thanks in advance for your suggestions!

Jochen

Hi @jochen. Thanks for your question. DEXSeq does the testing on flattened exon annotation (also called disjoint bins) based on all the transcript isoforms annotated to the gene. Please check the DEXSeq paper or the ?disjointExons for details, but that's why you have more exon bins than exons. Seems that you are only interested in the exons of the canonical isoform of ZEB2? if that's the case I'd recommend inputing a gtf file containing only that isoform.