The electrification of bicycles has introduced new dynamics to cycling, raising questions about how the pedal assistance of electric bikes (e-bikes) influences cyclists' route choice preferences. Understanding these preferences is crucial for developing cycling infrastructure that effectively supports the growing use of e-bikes. This paper develops a route choice framework to examine e-bike users' route preferences and compare them to those of regular cyclists, using GPS data from the E-Biking in Switzerland (EBIS) project. From the recorded trajectories 64,340 cycling trips are map-matched by using a trajectory segmentation map-matching algorithm. A data-driven path identification (DDPI) approach is employed to identify the choice set including only observed routes. A Path Size Logit (PSL) model is then estimated to identify the key determinants of e-bike users' route choices, considering factors such as gradient, type of bike facility, traffic conditions, intersections, age, and seasonal variations. To determine how e-bike users' route preferences differ from those of regular cyclists, segmented models will first be estimated separately for each bike type, followed by a pooled model. The findings will provide a comprehensive understanding of how the electrification of bicycles influences cyclists' route choice behavior, offering policymakers and transport planners valuable insights to the needs of different types of cyclists.