Can tophat2 align reads with lengths = 6bp? If not, which tool can?
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?
Maybe you should look at blast , i don't think you are interest into spliced alignment with 6 read length ....
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