zhangzhen/bulkfoodiepipeline is a bioinformatics pipeline used for in-vivo bulk FOODIE sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads, computes conversion rates of cytosines, and calls footprints of transcription factors.
2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.
Now, you can run the pipeline using:
nextflow run zhangzhen/bulkfoodiepipeline \
-profile conda \
--input samplesheet.csv \
--depth <NUM> \
--expected_ratio_file <EXPECTED_RATIO_FILE> \
--outdir <OUTDIR>Warning
Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.
zhangzhen/bulkfoodiepipeline was originally written by Zhang Zhen, Shen Ke, Wang Quangui.
We thank the following people for their extensive assistance in the development of this pipeline:
- group members at Sunney Xie Lab
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use bulk-foodie-pipeline for your analysis, please cite the FOODIE article as follows:
R. He, W. Dong, Z. Wang, C. Xie, L. Gao, W. Ma, K. Shen, D. Li, Y. Pang, F. Jian, J. Zhang, Y. Yuan, X. Wang, Z. Zhang, Y. Zheng, S. Liu, C. Luo, X. Chai, J. Ren, Z. Zhu, & X.S. Xie, Genome-wide single-cell and single-molecule footprinting of transcription factors with deaminase, Proc. Natl. Acad. Sci. U.S.A. 121 (52) e2423270121, doi: 10.1073/pnas.2423270121 (2024).
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.