Atmospheric escape of close-in exoplanets can be driven by high energy radiation from the host star. The planetary outflows interacting with the stellar wind may generate observable transit signals that depend on the strength of the stellar wind. We perform radiation-hydrodynamics simulations of the atmospheric escape of hot Jupiters with including the wind from the host star in a self-consistent, dynamically coupled manner. We show that the planetary outflow is shaped by the balance between its thermal pressure and the ram pressure of the stellar wind. We use the simulation outputs to calculate the Lyman-$\alpha$ and H$\alpha$ transit signatures. The transit peak depth is blue-shifted by $\sim 10km/s$, but strong winds can confine the outflow and decrease the Lyman-$\alpha$ transit depth. Contrastingly, the wind effect on H$\alpha$ is weak because of the small contribution from the uppermost atmosphere of the planet. The atmospheric mass-loss rate is approximately independent of the strength of the wind. We also discuss the effect of the flare on the transit signature, to conclude that the probability of a flare that would change the Lyman-$\alpha$ transit depth significantly during a single observation is low for solar-type host stars.