Bowtie Fp And Fn - How To Find ?

Question

[Arpssss]

I am using BowTie 1 to find alignments of 150 bp reads. Can anybody help me how to find how much False Positive and False Negative it gave ?

Answer 1

[Arun]

Well in reality, there's no way of knowing it. However to assess the performance of softwares (probably, to choose the best, if you wish), you could simulate data (you would then know the expression of every "expressed" transcript and location of every read corresponding to that transcript) using softwares like flux-simulator and map it using your favorite softwares and get an estimate the percentage of FP.