Dear Gordon, I am analyzing Rna- Seq data. In my data I have many transcripts that map to same gene. In order to avoid that I considered taking transcripts with greatest number of exons for each gene. (As describe in user manual of edge R). However there are multiple transcripts with same number of exons. Would you recommend best strategy to consider in this case? Should I sum all count data for those exon (as number of exon are same) and consider the highest one? Secondly, to achieve statistical significance for DE is there arbitrary values to filter tags? Thanks, Kuntal [[alternative HTML version deleted]]