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Optional downstream motif analyses included.\nStarting point are deduplicated BAM and/or CRAM files.\n\n## Important\n\nAll samples in a 'run' have to belong to the same group. That means that out of all peaks/sample, a union will be made. In case this is not the case, you can run the workflow multiple times.\nFasta headers are not allowed to contain a pipe character '|' (as peaks will be delimited as such later on).\n\n## Installation\n\nFrom pypi:\n\u003e  pip install ATACofthesnake  \n\nor with uv:\n\u003e  uv pip install ATACofthesnake  \n\nFrom github:\n\u003e  git clone git@github.com:maxplanck-ie/ATACofthesnake.git  \n\u003e  pixi run ATAC -h  \n\n\n## Quickstart\n\n \u003e ATAC -h\n\nBare minimum needed input:\n - directory with deduplicated bam and/or cram files.  \n - genome fasta file  \n - genome annotation file (GTF format)  \n - read attracting regions (BED format), this is necessary and needs to contain at least the full mitochondrial chromosome.  \n\nFor more details and how-to on requesting specific differential analysis and comparisons, please refer to the [documentation](https://atacofthesnake.readthedocs.io/en/stable/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxplanck-ie%2Fatacofthesnake","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaxplanck-ie%2Fatacofthesnake","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxplanck-ie%2Fatacofthesnake/lists"}