Hi, I have been wondering this for a while, but can't seem to find an answer.
I wanted to map my reads in TopHat with a maximum of 2 mismatches in the entire (100bp) read. In galaxy, I set "Number of mismatches allowed in each segment alignment for reads mapped independently = 2" which seems to correspond to "--segment-mismatches". So does that mean that if segment length is se to default (25), then for my 100bp reads the maximum number of mismatches could be up to 8? This is how I ran my analysis, but after re-reading the Tophat documentation it seems like this might not be giving me what I want. Based on the documentation, it sounds like in order to get max 2 mismatches along the entire 100bp, it would be done by setting --read-mismatches to 2. But I see no option to set --read-mismatches in galaxy.
Is there a way for me to set '--read-mismatches' on galaxy? Or should I set my segment length to 100 and just leave "--segment-mismatches" set to 2? Or is it fine the way I did it, and I'm just misunderstanding something?