Marker code is an effective coding scheme to protect data from insertions and deletions. It has potential applications in future storage systems, such as DNA storage and racetrack memory. When decoding marker codes, perfect channel state information (CSI), i.e., insertion and deletion probabilities, are required to detect insertion and deletion errors. Sometimes, the perfect CSI is not easy to obtain or the accurate channel model is unknown. Therefore, it is deserved to develop detecting algorithms for marker code without the knowledge of perfect CSI. In this paper, we propose two CSI-agnostic detecting algorithms for marker code based on deep learning. The first one is a model-driven deep learning method, which deep unfolds the original iterative detecting algorithm of marker code. In this method, CSI become weights in neural networks and these weights can be learned from training data. The second one is a data-driven method which is an end-to-end system based on the deep bidirectional gated recurrent unit network. Simulation results show that error performances of the proposed methods are significantly better than that of the original detection algorithm with CSI uncertainty. Furthermore, the proposed data-driven method exhibits better error performances than other methods for unknown channel models.