{ "info": { "author": "Xiannian Zhang", "author_email": "friedpine@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3.6", "Topic :: Software Development :: Build Tools" ], "description": "# DropRNA\n\n## Install baseq_drops\nWe need python3 and a package called: baseq_drops, which could be installed by:\n\n pip install baseqdrops\n\nAfter install, you will have a runnable command `baseq-Drop`\n\n## Config file\n\nThe pipeline need the following software or resources:\n\n+ `star`: STAR software, for fast alignment of RNA-Seq data;\n+ `samtools`: Sorting bam file;\n+ `whitelistDir`: The barcode whitelist files for indrop and 10X should be placed under whitelistDir.\nThese files can be downloaded from XXX.\n+ `cellranger_ref_`: The key process of read alignment and tagging to genes\n are inspired and borrowed from the open source cellranger pipeline\n (https://github.com/10XGenomics/cellranger).\n The refernces of genome index and transcriptome can be downloaded\n from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest.\nIn the config file, the directory of cellrange references is named as `cellranger_`.\n\nWhile running command, the configures are recorded in the file called `config_drops.ini`:\n\n [Drops]\n samtools = /path/to/samtools\n star = /path/to/STAR\n whitelistDir = /path/to/whitelist_file_directory\n cellranger_hg38 = /path/to/reference/refdata-cellranger-GRCh38-1.2.0/\n\n## Process Steps\n1. `Extract the Cell Barcode` Counting the number of each kinds of barcode; this will genrate a barcode_count..csv;\n2. `Cell Barcode correction and filtering` Correcting the cell barcode with 1bp mismatch, filtering the barcode with min number of reads;\n3. `Split the reads of valid Cell Barcodes` The raw pair-end raw reads are splitted to 16 single end files for multiprocessing according to the 2bp prefix of barcode; For example, we will get: split...fq\n4. `Star Alignment` Fastq files runs at the same time; The bam file sorted by sequence header is generated;\n5. `Reads tagging` Tagging the reads alignment position to the corresponding gene name\n6. `Genrating UMI table`\n\n## Run Command\n\nThe main config is:\n\n+ `--config`: config file;\n+ `--genome/-g`: genome version;\n+ `--protocol`: [10X|indrop|dropseq]\n+ `--minreads`: Minimum reads for a barcode\n+ `--name/-n` : Sample name\n+ `--fq1/-1`: Read 1\n+ `--fq2/-2`: Read 2\n+ `--top_million_reads`: How many million reads to use, mainly for testing pipeline with fraction of reads (default 1000)\n+ `--dir/-d`: output path\n\nIf you config the: `cellranger_ref_hg38` you can run the following:\n\n baseqdrops run_pipe --config ./config_drops.ini -g hg38 -p 10X --minreads 10000 -n 10X_test -1 10x_1.1.fq.gz -2 10x.2.fq.gz -d ./\n\n### For older version 10X results\nThe cell barcode length is 15 and UMI length is 5.\n\n baseqdrops run_pipe --config ./config_drops.ini -g hg38 -p 10X --minreads 10000 -n 10X_test -1 10x_1.1.fq.gz -2 10x.2.fq.gz -d ./\n\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://www.beiseq.com", "keywords": "sample setuptools development", "license": "", "maintainer": "", "maintainer_email": "", "name": "baseqRNA", "package_url": "https://pypi.org/project/baseqRNA/", "platform": "", "project_url": "https://pypi.org/project/baseqRNA/", "project_urls": { "Homepage": "https://www.beiseq.com" }, "release_url": "https://pypi.org/project/baseqRNA/1.5/", "requires_dist": [ "click", "configparser", "matplotlib", "numpy", "pandas", "check-manifest; 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