Cut_And_Run_Analysis_SnakeMake processes short whole-genome sequencing reads from Cut&Run. The pipeline generates trimmed fastq files, genome alignments, coverage files, and peak calls. To enable step-by-step data processing, we describe each of the individual data processing steps. We provide a Snakemake pipeline with clearly defined dependencies and Anaconda environments to automate the pipeline. We include a compact dataset in the repository that you may use to test the pipeline. We also provide an example detailing how Cut_And_Run_Analysis_SnakeMake can be used to process publicly available Cut&Run data. The original workflow was provided courtesy of the Sansam Lab.
- Requirements
- Description of individual steps in pipeline
- Step-by-step instructions on running Snakemake pipeline:
- Citations
- License
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Zang, C., Schones, D. E., Zeng, C., Cui, K., Zhao, K., & Peng, W. (2009). A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics, 25(15), 1952–1958. https://doi.org/10.1093/bioinformatics/btp340
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., & Liu, X. S. (2008). Model-based analysis of chip-seq(Macs). Genome Biology, 9(9), R137. https://doi.org/10.1186/gb-2008-9-9-r137
Amemiya, H. M., Kundaje, A., & Boyle, A. P. (2019). The encode blacklist: Identification of problematic regions of the genome. Scientific Reports, 9(1), 9354. https://doi.org/10.1038/s41598-019-45839-z
Boyle, A. (2018). Boyle-lab/blacklist: Official encode blacklist release for publication. Zenodo. https://doi.org/10.5281/ZENODO.1491733
Köster, J., & Rahmann, S. (2012). Snakemake—A scalable bioinformatics workflow engine. Bioinformatics (Oxford, England), 28(19), 2520–2522. https://doi.org/10.1093/bioinformatics/bts480
Anaconda Software Distribution. (2020). Anaconda Documentation. Anaconda Inc. Retrieved from https://docs.anaconda.com/
Provenance for blacklist file(s)
Amemiya, H.M., Kundaje, A. & Boyle, A.P. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Sci Rep 9, 9354 (2019). https://doi.org/10.1038/s41598-019-45839-z https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg19-blacklist.v2.bed.gz