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        "author": "Anthony Aylward",
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        "description": "# tssenrich\n\nCalculate [TSS enrichment](https://www.encodeproject.org/data-standards/terms/#enrichment) for ATAC-seq data. (see also the [ENCODE standards](https://www.encodeproject.org/atac-seq/))\n\n## Installation\n```\npip3 install tssenrich\n```\nor\n```\npip3 install --user tssenrich\n```\n\n## Usage\n```\nusage: tssenrich [-h] [--genome {hg38,hg19,mm10}] [--memory <float>]\n                 [--processes <int>] [--mapping-quality <int>]\n                 [--samtools-path <path/to/samtools>]\n                 [--log <path/to/log.txt>] [--tmp-dir <temp/file/dir/>]\n                 [--flank-distance <int>] [--flank-size <int>]\n                 <path/to/file.bam> [<path/to/file.bam> ...]\n\ncalculate TSS enrichment for ATAC-seq data\n\npositional arguments:\n  <path/to/file.bam>    Path to input BAM file\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --genome {hg38,hg19,mm10}\n                        genome build [hg38]\n  --memory <float>      memory limit in GB [2]\n  --processes <int>     number of processes/threads to use [1]\n  --mapping-quality <int>\n                        ignore reads with mapping quality below the given value [0]\n  --samtools-path <path/to/samtools>\n                        path to an alternate samtools executable [/usr/local/bin/samtools]\n  --log <path/to/log.txt>\n                        path to log file\n  --tmp-dir <temp/file/dir/>\n                        directory to use for temporary files\n  --flank-distance <int>\n                        distance from tss of outer ends of flanks [1000]\n  --flank-size <int>    size of flanks (for determining average depth) [100]\n\nENCODE standards:\n| Genome | Concerning | Acceptable | Ideal |\n| ------ | ---------- | ---------- | ----- |\n| hg19   | < 6        | 6 - 10     | > 10  |\n| hg38   | < 5        | 5 - 7      | > 7   |\n| mm10   | < 10       | 10 - 15    | > 15  |\n```\n\n## Examples\n```sh\ntssenrich example.bam > score.txt\n```\n\n```sh\ntssenrich --genome hg19 --log log.txt --memory 2 --processes 2 example1.bam example2.bam > scores.txt\n```\n\n\n",
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