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We have been using FluxSimulator successfully to simulate paired= -end reads of up to 100nt, using uniformly random (UR) fragmentation. = However, the 200nt fragment size limitation makes it difficult to try long= er read lengths (such as 120nt or 150nt) as we anticipate continued improve= ments in sequencing technology.
Would it be possible for us to "fool" the simulator into using longer fr= agments with UR fragmentation to generate longer paired-end reads? Or= would it be better to abandon UR fragmentation in favor of another kind?&n= bsp; We would like our simulations to be directly comparable so that read l= ength is the only variable that changes. At the same time, we would l= ike our simulations to reflect the kind of experiments people really are (o= r will be) doing.