Tophat 2.0.0 and option -r --mate-inner-dist

[EGrassi]

Hello, I'm wondering if the -r option is no longer required and why when using Tophat to align paired reads. The online manual describe it as required but in the Nature Protocols article[1] the example does not use it:
$ tophat -p 8 -G genes.gtf -o C1_R1_thout genome C1_R1_1.fq C1_R1_2.fq
I've launched it without this option and it's running peacefully...

Could someone point me in the right direction to understand what's changed and if it's better to give this parameter or not?

Thanks,
E.

[EGrassi]

Sorry, I read the beggining of the correct thread and abandoned just a sec before finding the right message (http://seqanswers.com/forums/showpos...0&postcount=32).
It says:

TopHat doesn't have much need for the mean inner distance nowadays, and will even less in the future, according to Cole Trapnell

OK, I get it, but why is that?
Unluckily with my hardware dotation it's not that easy to just run it multiple times with different parameters to compare the results...