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https://github.com/y9c/pseudou-bidseq

🧪 New pipeline for detecting pseudouridine modification on RNA (BID-seq, etc)
https://github.com/y9c/pseudou-bidseq

epitranscriptome epitranscriptomics modification mrna pseudouridine rna rrna single-base

Last synced: 2 days ago
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🧪 New pipeline for detecting pseudouridine modification on RNA (BID-seq, etc)

Host: GitHub
URL: https://github.com/y9c/pseudou-bidseq
Owner: y9c
License: gpl-3.0
Created: 2022-03-13T01:06:26.000Z (over 2 years ago)
Default Branch: main
Last Pushed: 2024-05-08T20:20:05.000Z (6 months ago)
Last Synced: 2024-05-08T21:33:20.261Z (6 months ago)
Topics: epitranscriptome, epitranscriptomics, modification, mrna, pseudouridine, rna, rrna, single-base
Language: Python
Homepage: https://bidseq.chuan.science/
Size: 11.6 MB
Stars: 11
Watchers: 1
Forks: 2
Open Issues: 2
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        [![Docker](https://img.shields.io/docker/pulls/y9ch/bidseq.svg)](https://hub.docker.com/r/y9ch/bidseq)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8158036.svg)](https://doi.org/10.5281/zenodo.8158036)

# Ψ-BID-seq

## Overview of the workflow



  

    

  

  

    

  



## How to use it?

A [docker image](https://hub.docker.com/r/y9ch/bidseq) containing the source code and dependencies has been published for reproducibility. You can run it using the [apptainer](https://apptainer.org/help) container runtime.

The entire analysis can be completed in just three steps:

1. **Specific the path of references (_.fasta_) and samples (_.fastq_) in a configure file (_.YAML_).**

   

     data.yaml for example^{(Click to expand)}

   ```yaml

   reference:

     contamination:

       fa: ./ref/contamination.fa

     genes:

       fa: ./ref/genes.fa

     genome:

       fa: /data/reference/genome/Mus_musculus/GRCm39.fa

       star: /data/reference/genome/Mus_musculus/star/GRCm39.release108

   samples:

     mESCWT-rep1-input:

       data:

         - R1: ./test/IP16.fastq.gz

       group: mESCWT

       treated: false

     mESCWT-rep1-treated:

       data:

         - R1: ./test/IP4.fastq.gz

       group: mESCWT

       treated: true

     mESCWT-rep2-treated:

       data:

         - R1: ./test/IP5.fastq.gz

       group: mESCWT

       treated: true

   ```

   You can copy and edit from this [template](test/data.yaml).

   _Read the [documentation](https://y9c.github.io/pseudoU-BIDseq/Step-by-step-instruction.html#define-settings-in-the-configure-file) on how to customize._

   

2. **Run all the analysis by one command**:

   ```bash

   apptainer run docker://y9ch/bidseq

   ```

   

       The pipeline will load configure file named `data.yaml` under the current directory.^{(Click to expand)}

   - Customized configure file with `-c` argument. (default: `data.yaml`)

   - Customized number of jobs/cores in parallel `-j` argument. (default: `48`)

   

3. **View the analytics reports and filtered sites.**

   

      3 folders are will be created in the working directory (default: `workspace`).^{(Click to expand)}

   

   ├── align_bam

   ├── report_reads

   └── filter_sites

   

   - trimming, mapping, and deduping reports are in `report_reads` folder, with key numbers in all the steps reported in one webpage^{([example](https://y9c.github.io/pseudoU-BIDseq/readsStats))}.

   - filtered sites for Ψ detection are in the `filter_sites` folder. These sites are only passed the _simplest filtering_, you can apply customized thresholds to them based on your data type and quality.

   - processed mapping results (_.bam_) are in `align_bam` folder. You can zoom into a location that you are interested in IGV.

   

## Documentation

[Read more](https://y9c.github.io/pseudoU-BIDseq)

## Citation

- cite this software

  ```BibTex

  @misc{y_y9cpseudou-bidseq_2022,

    title = {y9c/{pseudoU}-{BIDseq}: v1.0},

    url = {https://zenodo.org/record/8158036},

    urldate = {2023-07-18},

    publisher = {Zenodo},

    author = {Ye, Chang},

    month = dec,

    year = {2022},

    doi = {10.5281/zenodo.8158036},

  }

  ```

- cite the protocol

  ```BibTex

  @article{dai2023quantitative,

  title={Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution},

  author={Dai, Qing and Zhang, Li-Sheng and Sun, Hui-Lung and Pajdzik, Kinga and Yang, Lei and Ye, Chang and Ju, Cheng-Wei and Liu, Shun and Wang, Yuru and Zheng, Zhong and others},

  journal={Nature Biotechnology},

  volume={41},

  number={3},

  pages={344--354},

  year={2023},

  publisher={Nature Publishing Group US New York}

  }

  ```

- cite the method

  ```BibTex

  @article{dai_quantitative_2022,

    title = {Quantitative sequencing using {BID}-seq uncovers abundant pseudouridines in mammalian {mRNA} at base resolution},

    issn = {1087-0156},

    doi = {10.1038/s41587-022-01505-w},

    journal = {Nature Biotechnology},

    author = {Dai, Qing and Zhang, Li-Sheng and Sun, Hui-Lung and Pajdzik, Kinga and Yang, Lei and Ye, Chang and Ju, Cheng-Wei and Liu, Shun and Wang, Yuru and Zheng, Zhong and Zhang, Linda and Harada, Bryan T. and Dou, Xiaoyang and Irkliyenko, Iryna and Feng, Xinran and Zhang, Wen and Pan, Tao and He, Chuan},

    year = {2022},

    pages = {1--11},

  }

  ```

 



  





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