{ "info": { "author": "Emanuel Burgos", "author_email": "eburgos@wisc.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: MacOS X", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "[![Build Status](https://travis-ci.com/eburgoswisc/barseq.svg?branch=master)](https://travis-ci.com/eburgoswisc/barseq)\n![Python 3.7](https://img.shields.io/badge/python-3.7-blue.svg)\n\n# barseq \n\nPython package for analyzing barseq data.\n\n### Installation\n\n```bash\npip install git+https://github.com/mjmlab/barseq.git@master\n``` \n\n### Usage\n\n```bash\nbarseq -i -b -e \n```\n\n`-i` / `--input`\n\n- Directory with Illumina reads in either fastq or fastq.gz.\n\n\n`-b` / `--barcodes`\n\n- CSV file with barcode and correspondent gene names.\n\n\n`-e` / `--experiment`\n\n- Name of experiment, it is used for creating results folder.\n\n### Files Needed\n\n**Directory of Illumina reads [`-i`]** for analyzing. Can be either fastq or fastq.gz format\n\n```text\n@M06026:87:000000000-D69HY:1:1102:15909:1336 1:N:0:TGACCA\nCTCTAGAAAGTATAGGAACTTCAGGGCCATTTATATACCTTCCACTCTTCAACCGTGTCTTGACTTGACCTGGATGTCTCTACTGCTGTCATGCTACGTAGCTCATGCTACGTCGATCTAGTCGATGCATGCTAGCTGATCGACTCTCTTC\n+\nA#>>>3AA2DD>FBFGBFBFBFDDFGGAAEEEHDHFFFDDDBDGDFDDDDDADFGFFDDBFFEBFD5DFEEBBADABFGFGBBFGDD5BF3F43B3F1/11B144BGEBF@BBFB0B0BBFBBBBBBBB?E/FGFBB?/???B???/?FGG\n```\n\n**Barcode file [`-b`]** with gene names. Needs to be in CSV format.\n\n```text\nBarcode,Gene\nATGAAGACTGTTGCCGTA,WT\nCACGACGCCCTCCGCGGA,gene1\nACTATTACGCAAAATAAT,gene2\nATGGAAGATATTATTATT,gene3\nCCTCTCCAACCGGGTCTG,gene4\nCCCGGTCGCCTAGCCCCG,gene5\nGGCCCCCCGCCCGTCCCC,gene6\nGGATCACTGCTAGCGTAT,gene7\nCCTGCAGCAGCGGCCCGC,gene8\nACACATGCAGACATAGAG,gene9\nCGCGCCATCCGCCGCCCA,gene10\nAATATTCAGATGGGACGT,gene11\n```\n\n### Output\n\n#### `results/` directory\n\n- _results.csv: barcode counts found in each sequence file.\n\n\n| Gene | Barcode | Sample 1 | Sample 2 | Sample 3 | ... |\n| ---- | -------------------- | --------:| --------:| --------:| --- |\n| gene1| `ATGAAGACTGTTGCCGTA` | 500 | 5 | 7 | ... |\n| gene2| `CACGACGCCCTCCGCGGA` | 12 | 13 | 19 | ... |\n| gene3| `ACTATTACGCAAAATAAT` | 13 | 11 | 10 | ... |\n|_other| _other | 28 | 40 | 29 | ... |\n\n\n\n### Barseq Workflow\n\n![barseq_diagram](docs/barseq_workflow.png)\n\n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { 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