Computational protocol for the identification of X-linked genes contributing to X chromosome upregulation from RNA-sequencing datasets

The X chromosome/autosome ratio has been widely used to profile XCU at the chromosomal level. However, this approach overlooks features of inside genes. Here, we present a computational protocol for the identification of X-linked genes contributing to X chromosome upregulation from RNA-sequencing datasets. We describe steps for selecting data, preparing software, processing data, and data analysis. This protocol quantifies the contribution value and contribution increment of each X-linked gene to XCU. For complete details on the use and execution of this protocol, please refer to Lyu et al. (2022).(1)