{"id":26049,"date":"2024-01-24T17:10:59","date_gmt":"2024-01-24T09:10:59","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26049"},"modified":"2024-01-24T17:11:01","modified_gmt":"2024-01-24T09:11:01","slug":"10xgenomics%e5%8d%95%e7%bb%86%e8%83%9e%e6%b5%8b%e5%ba%8f%e5%88%86%e6%9e%90%ef%bc%88%e4%ba%8c%ef%bc%89cell-ranger%e7%bb%93%e6%9e%9c%e6%8a%a5%e5%91%8a%e8%a7%a3%e8%af%bb","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26049","title":{"rendered":"10\u00d7genomics\u5355\u7ec6\u80de\u6d4b\u5e8f\u5206\u6790\uff08\u4e8c\uff09Cell Ranger\u7ed3\u679c\u62a5\u544a\u89e3\u8bfb"},"content":{"rendered":"

\u5c0f\u679c\u4e0a\u4e00\u671f\u5e26\u5927\u5bb6\u8fdb\u884c\u4e86\u5355\u7ec6\u80de\u6d4b\u5e8f\u5206\u6790\u7684\u5b9e\u6218\u6559\u5b66\u3002\u4ece\u73af\u5883\u642d\u5efa\u5f00\u59cb\uff0c\u5230\u4e0b\u8f7d\u6570\u636e\uff0c\u8dd1\u901a\u6d41\u7a0b\uff0c\u6700\u540e\u6210\u529f\u8f93\u51fa\u4e86\u7ed3\u679c\u3002\u8fd9\u671f\u5c0f\u679c\u6765\u5bf9\u7ed3\u679c\u8fdb\u884c\u8be6\u7ec6\u7684\u89e3\u8bfb\u3002<\/p>\n

\u7ed3\u679c\u6982\u51b5<\/h2>\n

\u7ed3\u679c\u5728\u6837\u672c\u540d\/out\u76ee\u5f55\u4e0b<\/p>\n

<\/p>\n

\u8fd9\u4e9b\u5c31\u662f\u8f93\u51fa\u7684\u7ed3\u679c\u6587\u4ef6\u3002<\/p>\n

web_summary.html<\/p>\n

\u7f51\u9875\u683c\u5f0f\u7684\u8f93\u51fa\u603b\u7ed3\uff0c\u4e0b\u4e00\u90e8\u5206\u6211\u4eec\u4f1a\u7528\u6d4f\u89c8\u5668\u6253\u5f00\u6765\u770b\u3002<\/p>\n

metrics_summary.csv<\/p>\n

Csv\u683c\u5f0f\u7684\u603b\u7ed3\u6458\u8981\uff0c\u91cc\u9762\u7684\u4fe1\u606f\u7f51\u9875\u7248\u90fd\u4f1a\u5305\u542b\u3002<\/p>\n

<\/p>\n

\u6bd4\u5982\u8fd9\u4e9b\u6570\u5b57\u4ece\u5de6\u5230\u53f3\u4f9d\u6b21\u662f\uff0c\u4f30\u8ba1\u67091231\u4e2a\u7ec6\u80de\uff0c\u7b49\u7b49<\/p>\n

possorted_genome_bam.bam<\/p>\n

possorted_genome_bam.bam.bai<\/p>\n

\u8fd9\u4e24\u4e2a\u6587\u4ef6\u662f\u6bd4\u5bf9\u540e\u751f\u6210\u7684bam\u683c\u5f0f\uff0c\u53ca\u5176\u7d22\u5f15bai\u6587\u4ef6\u3002Possorted\u610f\u4e3a\u6309\u7167position\u4f4d\u7f6e\u6765\u8fdb\u884c\u6392\u5e8f\u3002<\/p>\n

raw_feature_bc_matrix.h5<\/p>\n

barcode\u77e9\u9635\u3002H5\u6587\u4ef6\u4e3a\u8de8\u5e73\u53f0\u5b58\u50a8\u7684\u6570\u636e\u6587\u4ef6\uff0c\u53ef\u4ee5\u88ab\u5176\u4ed6\u7684\u8f6f\u4ef6\u8bfb\u53d6\u5206\u6790\u3002<\/p>\n

raw_feature_bc_matrix\/<\/p>\n

\u8be5\u76ee\u5f55\u4e0b\u662f\u539f\u59cb\u7684\u6570\u636e\u7ed3\u679c\uff0c\u5305\u542b\u4ee5\u4e0b\u6587\u4ef6\u3002<\/p>\n

<\/p>\n

\u540e\u7eed\u5f88\u591a\u8f6f\u4ef6\u4e0b\u6e38\u7684\u5206\u6790\u90fd\u662f\u57fa\u4e8e\u8fd9\u4e2a\u7ed3\u679c\u3002<\/p>\n

Barcode\u662f\u7ec6\u80de\u7684\u4fe1\u606f<\/p>\n

Features\u662f\u57fa\u56e0\u7684\u4fe1\u606f<\/p>\n

\u6240\u4ee5Matrix\u8fd9\u4e2a\u77e9\u9635\u53eb\u505afeature barcode\u77e9\u9635\uff0c\u5b83\u7684\u884c\u662f\u57fa\u56e0\u540d\uff0c\u5217\u662fbarcode\u6bcf\u4e2a\u5355\u7ec6\u80de\u3002<\/p>\n

filtered_feature_bc_matrix\/<\/p>\n

\u8fd9\u91cc\u6211\u4eec\u8981\u8fd9\u4e2a\u8fc7\u6ee4\u6389\u80cc\u666f\u540e\u7684\u7ed3\u679c\u3002<\/p>\n

analysis\/<\/p>\n

<\/p>\n

\u8be5\u76ee\u5f55\u4e3acellranger\u5206\u6790\u7684\u7ed3\u679c\u3002<\/p>\n

\u5b83\u505a\u7684\u5206\u6790\u6709\u805a\u7c7b\uff0c\u5dee\u5f02\u8868\u8fbe\uff0cpca\u4e3b\u6210\u5206\u5206\u6790\uff0ctsne\uff0cumap\u8fd9\u4e9b\u90fd\u6709\u3002<\/p>\n

cloupe.cloupe<\/p>\n

\u8fd9\u4e2a\u6587\u4ef6\u4e5f\u5f88\u91cd\u8981\uff0c\u53ef\u4ee5\u76f4\u63a5\u653e\u5230\u4e0a\u671f\u4e0b\u8f7d\u7684cloupe browser\u91cc\u4ea4\u4e92\u5f0f\u67e5\u770b\u3002<\/p>\n

\u603b\u7ed3\u62a5\u544a\u7eb5\u89c8<\/h2>\n

\u6253\u5f00web_summary.html\u6587\u4ef6<\/p>\n

\u4ee5\u4e0b\u662f\u8be5\u6837\u672c\u7684\u6d4b\u5e8f\u4fe1\u606f\u7edf\u8ba1\u4e0e\u5206\u6790\u62a5\u544a<\/p>\n

<\/p>\n

\u8fd9\u662f\u7f51\u9875\u7248\u7684\u7ed3\u679c\u603b\u7ed3\u3002\u4e00\u5171\u68c0\u6d4b\u52301231\u4e2a\u7ec6\u80de\uff0c\u6bcf\u4e2a\u7ec6\u80de\u5e73\u5747\u670954104\u6761reads\uff0c\u5e73\u5747\u6bcf\u4e2a\u7ec6\u80de\u68c0\u6d4b\u52303235\u4e2a\u57fa\u56e0\u3002<\/p>\n

<\/p>\n

\u6d4b\u5e8f\u6620\u5c04\u4e0e\u6837\u672c<\/h3>\n

\u6d4b\u5e8fSequencing\uff0cQ30\u670994%\u8bf4\u660e\u6d4b\u5e8f\u8d28\u91cf\u5f88\u597d\u3002<\/p>\n

\u6620\u5c04Mapping\uff0c\u670996.1%\u6bd4\u5bf9\u4e0a\u4e86\u57fa\u56e0\u7ec4\uff0c\u6bd4\u5bf9\u7ed3\u679c\u826f\u597d\u3002<\/p>\n

\u5355\u7ec6\u80de\u8d28\u63a7<\/h3>\n

\u8fd9\u90e8\u5206\u7684\u7ed3\u679c\u5f88\u91cd\u8981\u3002<\/p>\n

<\/p>\n

\u5c0f\u679c\u4e4b\u524d\u4ecb\u7ecd\u4e8610\u00d7genomics\u5e73\u53f0\u5206\u9009\u7ec6\u80de\u5305\u6837\u54c1\u7684\u6280\u672f\u539f\u7406\uff0c\u5176\u91c7\u7528\u4e86\u5fae\u6d41\u63a7GEM\u6280\u672f\u3002\u901a\u5e38\u60c5\u51b5\u4e0b\uff0c\u6bcf\u4e2a\u6cb9\u6ef4\u4f1a\u5305\u88f9\u4e00\u4e2a\u7ec6\u80de\u3002\u4f46\u6709\u5c0f\u6982\u7387\u4f1a\u5305\u88f9\u4e24\u4e2a\u7ec6\u80de\u6216\u591a\u4e2a\uff08\u5927\u91cf\u7684UMI\u6570\uff09\uff0c\u8fd8\u6709\u4e0d\u5305\u88f9\u7ec6\u80de\uff08\u7a7a\u8f7d\uff0c\u4e5f\u4f1a\u6709\u5c11\u91cf\u7684UMI\uff09\u3002\u800c\u6837\u672c\u6709\u65f6\u5019\u4f1a\u6709\u88c2\u89e3\u6b7b\u4ea1\u7684\u7ec6\u80de\uff0c\u7a7a\u8f7d\u7684GEM\u4f1a\u6355\u83b7\u6e38\u79bb\u7684RNA\uff0c\u8fd9\u90e8\u5206\u5c31\u662f\u80cc\u666f\uff08\u4e0a\u56fe\u7070\u8272\u7ebf\u7684\u90e8\u5206\uff09\u3002<\/p>\n

\u8fd9\u4e2a\u56fe\u7684\u6a2a\u5750\u6807\u662fbarcodes\u4e5f\u5c31\u662f\u7ec6\u80de\u6570\u76ee\uff0c\u6a2a\u5750\u6807\u662fUMI counts\u4e5f\u5c31\u662f\u6d4b\u5e8freads, \u8fc7\u4f4e\u7684reads\uff081-2\u4f4d\u6570\uff09\u5927\u6982\u7387\u6355\u83b7\u6e38\u79bbRNA\u3002Cell Ranger\u4f1a\u91c7\u7528\u7b97\u6cd5\u5c06\u5176\u8fc7\u6ee4\u6389\uff0c\u4fdd\u8bc1\u5355\u7ec6\u80de\u6570\u636e\u7684\u8d28\u91cf\u3002\u6700\u540e\u7559\u4e0b\u6765\u7684\u6570\u636e\u5c31\u662f\u4e0a\u56fe\u84dd\u8272\u7ebf\u90e8\u5206\u3002<\/p>\n

<\/p>\n

\u8fd9\u91cc\u662f\u7ec6\u80de\u4e2a\u90e8\u5206\u6307\u6807\u3002\u6bd4\u5982\u603b\u5171\u68c0\u6d4b\u5230\u7684\u57fa\u56e0\u657024694\u4e2a\uff0c\u6bcf\u4e2a\u7ec6\u80de\u7684\u57fa\u56e0\u4e2d\u4f4d\u65703235\uff0c\u6bcf\u4e2a\u7ec6\u80de\u7684UMI Counts\u4e2d\u4f4d\u6570\u7b49<\/p>\n

<\/p>\n

\u70b9\u51fbCells\u65c1\u7684\u95ee\u597d\uff0c\u662f\u5bf9\u5404\u9879\u6307\u6807\u7684\u8be6\u7ec6\u89e3\u91ca\u3002<\/p>\n

\u57fa\u56e0\u8868\u8fbe\u4fe1\u606f<\/h3>\n

t-SNE<\/h4>\n

<\/p>\n

(\u5de6\u56fe\uff09\u8fd9\u91cc\u663e\u793a\u7684\u662f\u6bcf\u4e2a\u7ec6\u80de\u6761\u5f62\u7801\u7684 UMI \u603b\u8ba1\u6570\u3002\u4e0e UMI \u6570\u91cf\u8f83\u5c11\u7684\u7ec6\u80de\u76f8\u6bd4\uff0cUMI \u6570\u91cf\u8f83\u591a\u7684\u7ec6\u80de\u53ef\u80fd\u5177\u6709\u8f83\u9ad8\u7684 RNA \u542b\u91cf\u3002\u8f74\u5bf9\u5e94\u4e8e t-SNE \u7b97\u6cd5\u4ea7\u751f\u7684\u4e8c\u7ef4\u5d4c\u5165\u3002\u5728\u8fd9\u4e2a\u7a7a\u95f4\u4e2d\uff0c\u76f8\u8ddd\u8f83\u8fd1\u7684\u7ec6\u80de\u5bf9\u6bd4\u76f8\u8ddd\u8f83\u8fdc\u7684\u7ec6\u80de\u5bf9\u5177\u6709\u66f4\u76f8\u4f3c\u7684\u57fa\u56e0\u8868\u8fbe\u8c31\u3002<\/p>\n

(\u53f3\u56fe\uff09\u8fd9\u662f\u81ea\u52a8\u805a\u7c7b\u7b97\u6cd5\u5c06\u6bcf\u4e2a\u7ec6\u80de\u6761\u5f62\u7801\u5206\u914d\u5230\u7fa4\u7ec4\u4e2d\u3002\u805a\u7c7b\u5c06\u5177\u6709\u76f8\u4f3c\u8868\u8fbe\u8c31\u7684\u7ec6\u80de\u7ec4\u5408\u5728\u4e00\u8d77\u3002\u8f74\u5bf9\u5e94\u4e8e t-SNE \u7b97\u6cd5\u4ea7\u751f\u7684\u4e8c\u7ef4\u5d4c\u5165\u3002\u5728\u8fd9\u4e2a\u7a7a\u95f4\u4e2d\uff0c\u76f8\u8ddd\u8f83\u8fd1\u7684\u7ec6\u80de\u5bf9\u6bd4\u76f8\u8ddd\u8f83\u8fdc\u7684\u7ec6\u80de\u5bf9\u5177\u6709\u66f4\u76f8\u4f3c\u7684\u57fa\u56e0\u8868\u8fbe\u8c31\u3002\u663e\u793a\u4ec5\u9650\u4e8e\u968f\u673a\u7684\u7ec6\u80de\u5b50\u96c6\u3002<\/p>\n

<\/p>\n

\u53f3\u4e0a\u89d2\u53ef\u4ee5\u9009\u62e9\u6839\u636eK-means\u5206\u7c7b\uff0cK\u4ee3\u8868\u5206\u7c7b\u7684\u6570\u76ee\u3002<\/p>\n

\u7ec6\u80de\u7c7b\u4e4b\u95f4\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0<\/h4>\n

<\/p>\n

\u8fd9\u4e2a\u8868\u662fcluster1\u76f8\u8f83\u4e8e\u5176\u4ed6\u7684Cluster\uff0c\u54ea\u4e9b\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u3002<\/p>\n

\u9971\u548c\u5ea6<\/h4>\n

<\/p>\n

\u8be5\u56fe\u663e\u793a\u4e86\u6d4b\u5e8f\u9971\u548c\u5ea6\u6307\u6807\u4e0e\u4e0b\u91c7\u6837\u6d4b\u5e8f\u6df1\u5ea6\uff08\u4ee5\u6bcf\u4e2a\u7ec6\u80de\u7684\u5e73\u5747\u8bfb\u6570\u8861\u91cf\uff09\u7684\u51fd\u6570\u5173\u7cfb\uff0c\u76f4\u81f3\u89c2\u5bdf\u5230\u7684\u6d4b\u5e8f\u6df1\u5ea6\u3002\u6d4b\u5e8f\u9971\u548c\u5ea6\u662f\u5bf9\u89c2\u5bdf\u5230\u7684\u6587\u5e93\u590d\u6742\u6027\u7684\u8861\u91cf\uff0c\u5f53\u6240\u6709\u8f6c\u5316\u7684 mRNA \u8f6c\u5f55\u672c\u90fd\u6d4b\u5e8f\u5b8c\u6bd5\u65f6\uff0c\u6d4b\u5e8f\u9971\u548c\u5ea6\u63a5\u8fd1 1.0\uff08100%\uff09\u3002\u66f2\u7ebf\u5728\u7ec8\u70b9\u9644\u8fd1\u7684\u659c\u7387\u53ef\u88ab\u89e3\u91ca\u4e3a\u589e\u52a0\u6d4b\u5e8f\u6df1\u5ea6\u540e\u6240\u83b7\u6536\u76ca\u7684\u4e0a\u9650\u3002\u865a\u7ebf\u753b\u5728\u5408\u7406\u63a5\u8fd1\u9971\u548c\u70b9\u7684\u503c\u4e0a\u3002<\/p>\n

\u6bcf\u4e2a\u7ec6\u80de\u7684\u57fa\u56e0\u4e2d\u4f4d\u6570<\/h4>\n

<\/p>\n

\u8be5\u56fe\u663e\u793a\u4e86\u6bcf\u4e2a\u7ec6\u80de\u57fa\u56e0\u4e2d\u4f4d\u6570\u4e0e\u4e0b\u91c7\u6837\u6d4b\u5e8f\u6df1\u5ea6\u7684\u51fd\u6570\u5173\u7cfb\uff08\u4ee5\u6bcf\u4e2a\u7ec6\u80de\u5e73\u5747\u8bfb\u6570\u8868\u793a\uff09\uff0c\u76f4\u81f3\u89c2\u5bdf\u5230\u7684\u6d4b\u5e8f\u6df1\u5ea6\u3002\u66f2\u7ebf\u5728\u7ec8\u70b9\u9644\u8fd1\u7684\u659c\u7387\u53ef\u4ee5\u89e3\u91ca\u4e3a\u5728\u6b64\u70b9\u4e4b\u540e\u589e\u52a0\u6d4b\u5e8f\u6df1\u5ea6\u6240\u80fd\u83b7\u5f97\u6536\u76ca\u7684\u4e0a\u9650\u3002<\/p>\n

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