Why does CuffDiff accept insert-size parameters?

[Bio.X2Y]

Hi,

Does anyone know why CuffDiff (part of the CuffLinks suite) accepts parameters for the expected distance between paired end reads, and also for the number of threads to be used for alignment e.g.

--inner-dist-mean
--inner-dist-std-dev
--num-threads

I was under the impression that CuffDiff doesn't do any alignment, and would have no use for these parameters?

Thanks.

[Bio.X2Y]

Hi,

If Cole is out there, it would be great to get your thoughts.

Does CuffDiff attempt to perform some form of alignment step?

Thanks!