y9c / m5c-ubsseq

Ultrafast bisulfite

m⁵C-UBSseq

Changelog

• 4/23/2024: rewrite code using polars

workflow

Citation

• cite this software

  @software{chang_y_2024_11046885,
      author    = {Chang Y},
      title     = {y9c/m5C-UBSseq: V0.1},
      publisher = {Zenodo},
      version   = {v0.1},
      doi       = {10.5281/zenodo.11046885},
      url       = {https://doi.org/10.5281/zenodo.11046885}
  }

• cite the method

  @article{dai_ultrafast_2024,
      title = {Ultrafast bisulfite sequencing detection of 5-methylcytosine in {DNA} and {RNA}},
      url = {https://www.nature.com/articles/s41587-023-02034-w},
      doi = {10.1038/s41587-023-02034-w},
      author = {Dai, Qing and Ye, Chang and Irkliyenko, Iryna and Wang, Yiding and Sun, Hui-Lung and Gao, Yun and Liu, Yushuai and Beadell, Alana and Perea, José and Goel, Ajay and He, Chuan},
      date = {2024-01-02},
  }

 

Copyright © 2021-present Chang Y

m5c-ubsseq's Issues

Could you please upload the TSV file from your test data for comparison?

Hello, I used deduplicated BAM file to call mutation and obtained the following TSV file, but it appears some issues. Could you please upload the TSV file from your test data for comparison?

About Python scripts in snakefile？

Hello, I couldn't find many Python scripts mentioned in the script. Could you please provide scripts for calculating p-values and filtering? Thank you very much.