Tophat2 Aligning extremely short reads

Question

[biogirl04]

Hi,

Can tophat2 align reads with lengths = 6bp? If not, which tool can?

Thanks!

[ATpoint]

I do not see how any alignment of a hexamer would be meaningful. Simply because of the stochastic reasons, any hexamer would have a large amouts of occurrences in the genome. What exactly are you trying to do any why?

[Titus]

Maybe you should look at blast , i don't think you are interest into spliced alignment with 6 read length ....