snakemake_ATACseq_spikein: a spike-in–normalized ATAC-seq Snakemake workflow

main @ 899e385

Citation

If you use this workflow in your research, please cite it. Use the "Cite this repository" button on the GitHub repository page (generated from CITATION.cff), or cite the archived release on Zenodo via the DOI badge above — the concept DOI always resolves to the latest version.

Please also cite the individual tools used:

• Snakemake: Köster, J. and Rahmann, S. (2012). Snakemake—a scalable bioinformatics workflow engine. Bioinformatics, 28(19), 2520-2522.
• MACS2: Zhang, Y. et al. (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biology, 9, R137.
• deepTools: Ramírez, F. et al. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research, 44(W1), W160-W165.
• Bowtie2: Langmead, B. and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357-359.
• SAMtools: Li, H. et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079.
• IDR: Li, Q. et al. (2011). Measuring reproducibility of high-throughput experiments. Annals of Applied Statistics, 5(3), 1752-1779.
• featureCounts (Subread): Liao, Y. et al. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930.
• Consensus peaks (fixed-width / score-per-million): Corces, M.R. et al. (2018). The chromatin accessibility landscape of primary human cancers. Science, 362(6413), eaav1898.
• BEDTools: Quinlan, A.R. and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-842.
• FastQC: Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data.
• fastp: Chen, S. et al. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884-i890.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contact

Author: gynecoloji
Project Repository: https://github.com/gynecoloji/snakemake_ATACseq_spikein

For questions, issues, or feature requests, please:

1. Check the existing Issues on GitHub
2. Submit a new issue with detailed information about your problem
3. Include relevant log files and system information for troubleshooting

Acknowledgments

This pipeline was developed based on best practices from the ENCODE consortium and incorporates methodologies from multiple published ATAC-seq analysis workflows. Special thanks to the developers of all the integrated tools that make this comprehensive analysis possible.

Note: This pipeline is optimized for human genome analysis (hg38) but can be adapted for other organisms by updating reference files and parameters.