DH has a seat fitted to his mountain bike, I think there are issues if you have rear suspension though.
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Personally I found it hard to get on and off the bike with the seat on, and I found it tricky lifting DS into it. Once I was going I was OK though. To me the huge advantage of the trailer is that I can carry stuff as well as the child. Even a quick trip to the playground usually means I'm carrying drinks, inhalors, snack, spare clothes etc. there is not a lot of space for a rucksack on my back and DS in the seat.
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Since you have the seat I would give it a go and see if you get on with it.