novoalign parameters_alignment scoring options

[sadiexiaoyu]

Dear All,

I am confusing about the parameter in novoalign, the -t, -g, -x, I read the manual, and it seems that these three parameters can be used for setting mismatch when you map your reads to the reference. However, how could I set them? Is there any way to calculate? How could I know which number should I set for the -t, -g, -x. I checked the forum, and I did not get it why eg. -t=60, then it is around 3 mismatch... Could anyone help me?

Thanks in advance!

Cheers,

Sadiexiaoyu