Hi,

1. Not sure if I ran Flux correctly or not, is it possible to simulate reads only containing exons? Both the simulated reads: the example Poly-dT Priming and Nebulization (A.thaliana) and my custom case contains reads having sequence from introns or UTRs, but I only want reads containing sequence from exons. The parameters I used to simulate are in the attachments. 
2. Is it possible to calculate sequencing coverage for the simulation? For example: Sum of (read number * read length) / Sum of (expressed number * transcript length)