About TEIRI

About

TEIRI is a pipeline to identify TE-initiated RNAs by integrating short-read RNA-seq, long-read RNA-seq, CAGE, and RAMPAGE datasets.

The upstream repository includes:

• Pipeline scripts: https://github.com/yunzhang1998/TEIRI/tree/main/scripts

• TE-initiated RNA annotation files: https://github.com/yunzhang1998/TEIRI/tree/main/annotation

Guides

• Installation

• Usage

• Example

License

See upstream license information: https://github.com/janky-yz/TEIRI/blob/main/LICENSE

Citation

If you use TEIRI in your research, please cite:

• Yun Zhang, Jianqi She, Xueyan Hu, Yueqi Jin, Jiaming Zhao, Songyan Hou, Changyu Tao, Minghao Du, Ence Yang. Transposable elements drive species-specific and tissue-specific transcriptomes in human development. Genome Biology, 2025, 26:379, https://doi.org/10.1186/s13059-025-03855-5