I am trying to change STAR parameters to decrease mismatch rate.
the parameters are going to be changed are:
--outFilterMismatchNmax --outFilterMismatchNoverLmax --outFilterMismatchNoverReadLmax
The one is going to be changed while the rest are the same as default. Then if I find the best value for the first one, I enter the first parameter with the best value and then change the second one and so on. Am I right ?
Then I will visualize the results. Which software do you recommend to use ?