Hi,

having a look at the TopHat manual you can easily find this information. Here are the relevant sections.

-m/--splice-mismatches <int> The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0.

--initial-read-mismatches Reads are initially mapped, allowing up to this many mismatches in each read alignment. The default is 2.

--segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2.

-n/--transcriptome-mismatches Maximum number of mismatches allowed when reads are aligned to the transcriptome.