{"id":67382,"date":"2026-11-14T20:02:28","date_gmt":"2026-11-14T12:02:28","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=67382"},"modified":"2026-11-14T20:48:15","modified_gmt":"2026-11-14T12:48:15","slug":"cell-ranger-raw-filtered-matrix-barcode-audit","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/cell-ranger-raw-filtered-matrix-barcode-audit\/","title":{"rendered":"Cell Ranger \u7ed9\u4e86\u4e24\u5957\u77e9\u9635\uff0c\u600e\u4e48\u786e\u8ba4\u5c11\u6389\u7684\u662f\u54ea\u4e9b\u6761\u5f62\u7801\uff1f"},"content":{"rendered":"
\n

\u540c\u4e00\u4e2a\u6587\u5e93\u8dd1\u5b8c Cell Ranger\uff0c\u539f\u59cb\u77e9\u9635\u91cc\u53ef\u80fd\u6709\u51e0\u5341\u4e07\u4e2a\u6761\u5f62\u7801\uff0c\u8fc7\u6ee4\u77e9\u9635\u91cc\u53ea\u5269\u51e0\u5343\u4e2a\u3002\u7b2c\u4e00\u6b21\u63a5\u624b\u6570\u636e\u7684\u4eba\u5e38\u95ee\uff0c\u662f\u6d4b\u5e8f\u4e22\u4e86\u7ec6\u80de\uff0c\u8fd8\u662f\u8f6f\u4ef6\u5220\u6389\u4e86\u57fa\u56e0\uff1f\u8fd9\u4e24\u4e2a\u76ee\u5f55\u56de\u7b54\u7684\u662f\u540c\u4e00\u6279\u5206\u5b50\u5c5e\u4e8e\u54ea\u4e9b\u6761\u5f62\u7801\uff0c\u53ea\u662f\u4ea4\u4ed8\u7ed9\u4e0b\u6e38\u7684\u6761\u5f62\u7801\u8303\u56f4\u4e0d\u540c\u3002\u9009\u4e00\u4e2a\u719f\u6089\u7684\u57fa\u56e0\uff0c\u9010\u4e2a\u6838\u5bf9\u5b83\u5728\u4fdd\u7559\u5217\u91cc\u7684\u8ba1\u6570\uff0c\u53ef\u4ee5\u628a\u8fd9\u4e2a\u95ee\u9898\u4ece\u731c\u6d4b\u53d8\u6210\u4e00\u9879\u6587\u4ef6\u68c0\u67e5\u3002<\/p>\n

\u4ee5\u4e0b\u4ee5\u5e38\u89c4\u57fa\u56e0\u8868\u8fbe\u6587\u5e93\u7684 cellranger count<\/code> \u8f93\u51fa\u4e3a\u4f8b\u3002\u591a\u6837\u672c\u62c6\u5206\u3001\u63a2\u9488\u578b\u6587\u5e93\u4ee5\u53ca\u989d\u5916\u505a\u8fc7\u73af\u5883\u6838\u7cd6\u6838\u9178\u6821\u6b63\u7684\u77e9\u9635\uff0c\u6587\u4ef6\u5c42\u7ea7\u548c\u7b5b\u9009\u542b\u4e49\u53ef\u80fd\u4e0d\u540c\u3002\u62ff\u5230\u5916\u90e8\u4ea4\u4ed8\u65f6\uff0c\u5148\u627e\u5206\u6790\u547d\u4ee4\u3001\u8f6f\u4ef6\u7248\u672c\u548c\u6587\u5e93\u7f16\u53f7\u3002\u76ee\u5f55\u540d\u90fd\u662f\u201c\u8fc7\u6ee4\u540e\u201d\uff0c\u4e5f\u6709\u53ef\u80fd\u4e00\u4e2a\u6765\u81ea\u539f\u59cb\u8f6f\u4ef6\uff0c\u53e6\u4e00\u4e2a\u5df2\u7ecf\u88ab\u5206\u6790\u4eba\u5458\u518d\u6b21\u8d28\u63a7\u3002<\/p>\n

\u5206\u6e05\u884c\u3001\u5217\u548c\u77e9\u9635\u91cc\u5b58\u7684\u503c<\/h2>\n

\u5728 outs<\/code> \u4e0b\u9762\u627e\u5230 raw_feature_bc_matrix<\/code> \u548c filtered_feature_bc_matrix<\/code>\u3002\u5404\u76ee\u5f55\u901a\u5e38\u542b\u538b\u7f29\u7684\u7279\u5f81\u8868\u3001\u6761\u5f62\u7801\u8868\u548c\u7a00\u758f\u77e9\u9635\u3002\u7279\u5f81\u8868\u7ed9\u884c\u7684\u8eab\u4efd\uff0c\u6761\u5f62\u7801\u8868\u7ed9\u5217\u7684\u8eab\u4efd\uff0c\u77e9\u9635\u91cc\u7684\u6574\u6570\u662f\u5f52\u5230\u67d0\u7279\u5f81\u548c\u67d0\u6761\u5f62\u7801\u7684\u53bb\u91cd\u5206\u5b50\u8ba1\u6570\u3002\u4e24\u4e2a\u76ee\u5f55\u5e94\u6210\u5957\u8bfb\u53d6\u3002\u62ff\u539f\u59cb\u77e9\u9635\u914d\u8fc7\u6ee4\u7248\u6761\u5f62\u7801\uff0c\u5373\u4f7f\u7a0b\u5e8f\u6ca1\u6709\u7acb\u523b\u62a5\u9519\uff0c\u5217\u53f7\u4e5f\u5df2\u7ecf\u5931\u53bb\u539f\u6765\u7684\u542b\u4e49\u300210x \u5bf9\u7279\u5f81\u4e0e\u6761\u5f62\u7801\u77e9\u9635\u7684\u8bf4\u660e<\/a><\/p>\n

\u539f\u59cb\u77e9\u9635\u4fdd\u7559\u7684\u662f\u6ee1\u8db3\u8be5\u6d41\u7a0b\u6761\u4ef6\u3001\u6709\u8bfb\u6bb5\u652f\u6301\u7684\u767d\u540d\u5355\u6761\u5f62\u7801\uff0c\u5176\u4e2d\u53ef\u80fd\u6709\u7ec6\u80de\uff0c\u4e5f\u53ef\u80fd\u53ea\u6709\u73af\u5883\u4e2d\u7684\u6e38\u79bb\u5206\u5b50\u3002\u8fc7\u6ee4\u77e9\u9635\u4fdd\u7559\u7684\u662f\u8f6f\u4ef6\u5224\u4e3a\u4e0e\u7ec6\u80de\u5173\u8054\u7684\u6761\u5f62\u7801\u3002\u56e0\u800c\u4e0d\u80fd\u628a\u4e24\u8005\u76f8\u51cf\u540e\u76f4\u63a5\u79f0\u4f5c\u201c\u6b7b\u6389\u7684\u7ec6\u80de\u6570\u201d\u3002\u5bf9\u540c\u4e00\u6b21\u5e38\u89c4\u8ba1\u6570\u8f93\u51fa\uff0c\u5e94\u8be5\u5148\u770b\u5230\u5217\u96c6\u5408\u6536\u7f29\uff0c\u518d\u9a8c\u8bc1\u4fdd\u7559\u5217\u4e0a\u7684\u8ba1\u6570\u80fd\u591f\u4e00\u4e00\u5bf9\u4e0a\u3002\u7279\u5f81\u8868\u6709\u65f6\u8fd8\u542b\u6297\u4f53\u7b49\u5176\u4ed6\u7c7b\u578b\uff0c\u8ba1\u7b97\u201c\u68c0\u6d4b\u5230\u591a\u5c11\u57fa\u56e0\u201d\u65f6\u5e94\u5148\u9650\u5b9a\u57fa\u56e0\u8868\u8fbe\u7279\u5f81\u3002<\/p>\n

\u7528\u56db\u5217\u6570\u636e\u770b\u61c2\u53d8\u5316\u53d1\u751f\u5728\u54ea\u91cc<\/h2>\n

\u8bbe\u539f\u59cb\u77e9\u9635\u53ea\u6709\u4e09\u4e2a\u57fa\u56e0\u548c\u56db\u4e2a\u6761\u5f62\u7801\u3002\u4e3a\u4e86\u6f14\u793a\uff0c\u5047\u8bbe\u8f6f\u4ef6\u4fdd\u7559\u4e86\u7b2c\u4e00\u3001\u7b2c\u4e09\u4e2a\u6761\u5f62\u7801\u3002\u8fd9\u4e2a\u8bbe\u5b9a\u53ea\u6f14\u793a\u5982\u4f55\u67e5\u6587\u4ef6\uff0c\u4e0d\u6a21\u62df\u8f6f\u4ef6\u5982\u4f55\u505a\u7ec6\u80de\u5224\u5b9a\u3002\u8868\u5185\u7684\u96f6\u4e5f\u8981\u8bfb\u8fdb\u53bb\uff0c\u4e00\u5217\u4e2d\u67d0\u4e2a\u57fa\u56e0\u4e3a\u96f6\uff0c\u53ea\u8868\u793a\u8be5\u7ec4\u5408\u6ca1\u6709\u8ba1\u5230\u5206\u5b50\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u6559\u5b66\u6761\u5f62\u7801<\/th>\n\u4e09\u4e2a\u57fa\u56e0\u7684\u8ba1\u6570<\/th>\n\u603b\u5206\u5b50\u6570<\/th>\n\u8fc7\u6ee4\u7ed3\u679c<\/th>\n<\/tr>\n<\/thead>\n
\u7532<\/td>\n5\u30011\u30010<\/td>\n6<\/td>\n\u4fdd\u7559<\/td>\n<\/tr>\n
\u4e59<\/td>\n1\u30010\u30010<\/td>\n1<\/td>\n\u672a\u4fdd\u7559<\/td>\n<\/tr>\n
\u4e19<\/td>\n0\u30013\u30012<\/td>\n5<\/td>\n\u4fdd\u7559<\/td>\n<\/tr>\n
\u4e01<\/td>\n1\u30010\u30011<\/td>\n2<\/td>\n\u672a\u4fdd\u7559<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u7532\u5217\u5728\u8fc7\u6ee4\u524d\u662f\u4e94\u3001\u4e00\u3001\u96f6\uff0c\u8fc7\u6ee4\u540e\u4ecd\u5e94\u662f\u8fd9\u4e09\u4e2a\u6570\u3002\u7b2c\u4e00\u884c\u57fa\u56e0\u7684\u5168\u77e9\u9635\u603b\u6570\u5374\u4f1a\u4ece\u4e03\u964d\u5230\u4e94\uff0c\u56e0\u4e3a\u4e59\u548c\u4e01\u5404\u8d21\u732e\u7684\u4e00\u4e2a\u5206\u5b50\u968f\u5217\u9000\u51fa\u3002\u57fa\u56e0\u6ca1\u6709\u4ece\u7279\u5f81\u8868\u6d88\u5931\uff0c\u4fdd\u7559\u7ec6\u80de\u7684\u8868\u8fbe\u503c\u4e5f\u6ca1\u6709\u88ab\u91cd\u65b0\u5f52\u4e00\u5316\u3002\u82e5\u6709\u4eba\u8bf4\u201c\u8fc7\u6ee4\u4f7f\u8fd9\u4e2a\u57fa\u56e0\u7684\u8868\u8fbe\u4e0b\u964d\u201d\uff0c\u5148\u8ffd\u95ee\u4ed6\u6bd4\u7684\u662f\u8be5\u57fa\u56e0\u8de8\u6240\u6709\u6761\u5f62\u7801\u7684\u603b\u548c\uff0c\u8fd8\u662f\u540c\u4e00\u4e2a\u7ec6\u80de\u4e2d\u7684\u6570\u3002\u8fd9\u4e2a\u4f8b\u5b50\u91cc\u53ea\u6709\u524d\u8005\u53d1\u751f\u4e86\u53d8\u5316\u3002<\/p>\n

\"4
\u6559\u5b66\u77e9\u9635\uff5c\u7532\u548c\u4e19\u88ab\u4fdd\u7559\uff0c\u884c\u8868\u793a\u540c\u4e00\u5957\u57fa\u56e0\u3002<\/figcaption><\/figure>\n

\u5728\u771f\u5b9e\u6587\u4ef6\u4e2d\u9a8c\u8bc1\u5217\u8eab\u4efd<\/h2>\n

\u8fdb\u5165\u540c\u4e00\u6587\u5e93\u7684 outs<\/code> \u76ee\u5f55\uff0c\u5728\u88c5\u6709 Python \u7684\u73af\u5883\u8fd0\u884c\u4e0b\u9762\u8fd9\u6bb5\u4ee3\u7801\u3002\u5b83\u53ea\u8bfb\u4e24\u4e2a\u538b\u7f29\u6761\u5f62\u7801\u6587\u4ef6\uff0c\u6253\u5370\u4e24\u7ec4\u5217\u6570\u3001\u8fc7\u6ee4\u7248\u72ec\u6709\u7684\u6570\u91cf\uff0c\u4ee5\u53ca\u539f\u59cb\u7248\u72ec\u6709\u7684\u6570\u91cf\u3002\u5982\u679c\u7b2c\u4e09\u9879\u5927\u4e8e\u96f6\uff0c\u5148\u628a\u6837\u672c\u3001\u5bfc\u51fa\u7684\u6d41\u7a0b\u548c\u6761\u5f62\u7801\u540e\u7f00\u6838\u5bf9\u6e05\u695a\uff0c\u518d\u7ee7\u7eed\u8bfb\u77e9\u9635\u3002\u5bf9\u8de8\u6587\u5e93\u5408\u5e76\u6570\u636e\uff0c\u672b\u5c3e\u7684\u540e\u7f00\u53ef\u80fd\u627f\u62c5\u533a\u5206\u6587\u5e93\u7684\u4f5c\u7528\uff0c\u4e0d\u8981\u4e3a\u4e86\u5bf9\u4e0a\u6570\u91cf\u76f4\u63a5\u5220\u9664\u3002<\/p>\n

import gzip\r\nfrom pathlib import Path\r\n\r\ndef barcodes(folder):\r\n    with gzip.open(Path(folder) \/ "barcodes.tsv.gz", "rt") as fh:\r\n        values = [line.strip() for line in fh]\r\n    assert len(values) == len(set(values))\r\n    return set(values)\r\n\r\nraw = barcodes("raw_feature_bc_matrix")\r\nkept = barcodes("filtered_feature_bc_matrix")\r\nprint(len(raw), len(kept), len(kept - raw), len(raw - kept))\r\n<\/code><\/pre>\n
\u96c6\u5408\u68c0\u67e5\u901a\u8fc7\u540e\uff0c\u518d\u62bd\u51e0\u4e2a\u4fdd\u7559\u6761\u5f62\u7801\u3002\u5148\u901a\u8fc7\u6761\u5f62\u7801\u8868\u627e\u5230\u5b83\u5728\u4e24\u4e2a\u76ee\u5f55\u4e2d\u5404\u81ea\u7684\u5217\u53f7\uff0c\u518d\u6309\u7a33\u5b9a\u7684\u7279\u5f81\u7f16\u53f7\u5bf9\u9f50\u884c\u3001\u9010\u9879\u6bd4\u8f83\u6570\u503c\u3002\u4e0d\u8981\u62ff\u57fa\u56e0\u7b80\u79f0\u5f53\u4f5c\u552f\u4e00\u952e\uff0c\u591a\u4e2a\u7279\u5f81\u53ef\u80fd\u62e5\u6709\u76f8\u540c\u7684\u663e\u793a\u540d\u79f0\u3002\u7a00\u758f\u77e9\u9635\u8fd8\u5bb9\u6613\u9020\u6210\u4e00\u4e2a\u89c6\u89c9\u9519\u89c9\uff0c\u6587\u4ef6\u53ea\u5199\u975e\u96f6\u9879\uff0c\u627e\u4e0d\u5230\u67d0\u4e2a\u201c\u884c\u53f7\u3001\u5217\u53f7\u201d\u7ec4\u5408\u901a\u5e38\u4ee3\u8868\u8be5\u5904\u4e3a\u96f6\u3002\u8fd9\u548c\u7279\u5f81\u538b\u6839\u6ca1\u6709\u8fdb\u5165\u53c2\u8003\u6ce8\u91ca\uff0c\u662f\u4e24\u79cd\u9700\u8981\u5206\u522b\u8bb0\u5f55\u7684\u60c5\u51b5\u3002<\/p>\n
\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u516c\u5f00 PBMC \u6570\u636e\u7684\u539f\u77e9\u9635\u6709\u591a\u5c11\u5217\u771f\u7684\u6709\u5206\u5b50<\/h2>\n
\u6211\u4eec\u4e0b\u8f7d\u4e86 10x \u516c\u5f00\u7684\u4e00\u5343\u4e2a\u5916\u5468\u8840\u5355\u4e2a\u6838\u7ec6\u80de\u793a\u4f8b\u7684\u4e24\u4efd HDF5 \u6587\u4ef6\uff0c\u4f7f\u7528 h5py 3.16.0 \u548c\u7a00\u758f\u77e9\u9635\u9010\u5217\u6838\u5bf9\u3002\u5382\u5546\u7684 Cell Ranger 3.0.0 \u539f\u59cb\u8f93\u51fa\u6709 33,538 \u4e2a\u7279\u5f81\u30016,794,880 \u4e2a\u6761\u5f62\u7801\u5217\uff0c\u8fc7\u6ee4\u77e9\u9635\u4fdd\u7559\u76f8\u540c\u7684\u7279\u5f81\u548c 1,222 \u4e2a\u6761\u5f62\u7801\u3002\u5728\u539f\u8868\u4e2d\u6309\u5b9e\u9645\u5b57\u7b26\u4e32\u91cd\u65b0\u5b9a\u4f4d\u8fd9 1,222 \u5217\uff0c\u6240\u6709\u57fa\u56e0\u4e0e\u6761\u5f62\u7801\u7ec4\u5408\u7684\u8ba1\u6570\u5dee\u5f02\u5747\u4e3a\u96f6\u3002\u8fd9\u4e2a\u5b9e\u6d4b\u8986\u76d6\u8bfb\u53d6\u548c\u6838\u5bf9\u5382\u5546\u53d1\u5e03\u7684\u8ba1\u6570\u7ed3\u679c\uff0c\u672a\u91cd\u65b0\u4ece FASTQ \u8fdb\u884c\u6bd4\u5bf9\u300210x \u516c\u5f00 PBMC \u6837\u672c\u3001\u5b9e\u9a8c\u6761\u4ef6\u53ca\u8bb8\u53ef<\/a><\/p>\n
\u6570\u91cf\u6700\u5bb9\u6613\u770b\u9519\u7684\u662f\u8fc7\u6ee4\u6389\u7684\u90e8\u5206\u3002\u539f\u8868\u4e2d\u6709 6,793,658 \u4e2a\u6761\u5f62\u7801\u672a\u8fdb\u8fc7\u6ee4\u8868\uff0c\u5176\u4e2d\u53ea\u6709 233,378 \u4e2a\u81f3\u5c11\u6709\u4e00\u4e2a\u5206\u5b50\u3002\u4ec5\u539f\u8868\u4e2d\u51fa\u73b0\u7684\u6761\u5f62\u7801\u603b UMI \u4e2d\u4f4d\u6570\u662f\u96f6\uff0c\u6700\u9ad8\u5374\u8fbe\u5230 2,372\u3002\u672a\u4fdd\u7559\u5217\u65e2\u5305\u62ec\u5927\u91cf\u96f6\u5217\uff0c\u4e5f\u542b\u503c\u5f97\u8fdb\u4e00\u6b65\u590d\u6838\u7684\u975e\u96f6\u6761\u5f62\u7801\u3002\u7edf\u8ba1\u539f\u8868\u65f6\u628a\u201c\u6240\u6709\u5217\u201d\u201c\u975e\u96f6\u5217\u201d\u548c\u201c\u5224\u5b9a\u4e3a\u7ec6\u80de\u7684\u5217\u201d\u5206\u522b\u5199\u5f00\uff0c\u6bd4\u628a\u516d\u767e\u591a\u4e07\u5217\u76f4\u63a5\u53eb\u4f5c\u516d\u767e\u591a\u4e07\u4e2a\u6db2\u6ef4\u6216\u7ec6\u80de\u66f4\u51c6\u786e\u3002\u8f83\u9ad8\u7684\u672a\u4fdd\u7559\u8ba1\u6570\u672c\u8eab\u4f9d\u7136\u4e0d\u80fd\u8bc1\u660e\u5b83\u662f\u4e00\u679a\u5e94\u8be5\u6551\u56de\u7684\u7ec6\u80de\u3002<\/p>\n
\u7ec6\u80de\u6570\u504f\u4f4e\uff0c\u56de\u5230\u6392\u540d\u56fe\u5224\u65ad\u4e0b\u4e00\u6b65<\/h2>\n
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