RNA editing is an important post-transcriptional modification process. There are many algorithms used to identify RNA editing. This study of the sequencing depth’s effect on RNA editing will provide a suggested method for RNA editing research. Mouse reference genome was mapped to the RNA-seq by STAR. Then identified SNV by GATK, finally RNA Editing sites were filtered by Separate method, GIREMI and RNAEditor. The results showed the identification of RNA editing varied in three methods. There was little overlap in results. As the sequencing depth increases, the identified number of RNA editing sites also increases. In conclusion, the identification of RNA editing sites is positive correlated with the sequencing depth.