{"id":25283,"date":"2024-01-19T17:04:00","date_gmt":"2024-01-19T09:04:00","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25283"},"modified":"2024-01-19T17:04:01","modified_gmt":"2024-01-19T09:04:01","slug":"%e4%ba%94%e5%88%86%e9%92%9f%e6%95%99%e4%bd%a0%e8%a7%82%e7%9c%8bfastq%e6%96%87%e4%bb%b6%e8%b4%a8%e9%87%8f%e8%af%84%e4%bc%b0%e7%bb%93%e6%9e%9c","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25283","title":{"rendered":"\u4e94\u5206\u949f\u6559\u4f60\u89c2\u770bFASTQ\u6587\u4ef6\u8d28\u91cf\u8bc4\u4f30\u7ed3\u679c"},"content":{"rendered":"

\u4e66\u63a5\u4e0a\u56de\uff0c\u4e0a\u4e00\u6b21\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u4e86\u5982\u4f55\u8fdb\u884cFASTQ\u6587\u4ef6\u7684\u8d28\u91cf\u8bc4\u4f30\uff0c\u8fd9\u6b21\u5c31\u7ed9\u5927\u5bb6\u5206\u4eab\u4e00\u4e0b\u5982\u4f55\u89c2\u770b\u8d28\u91cf\u8bc4\u4f30\u7ed3\u679c\uff0c\u5c0f\u4f19\u4f34\u4eec\u8d76\u7d27\u5f80\u4e0b\u770b\u5427\u3002<\/p>\n

# \u53ef\u572801_clean\u8def\u5f84\u4e0b\u4f7f\u7528less\u547d\u4ee4\u9010\u4e00\u67e5\u770b\u6d4b\u5e8f\u6570\u636e\u8d28\u91cf\u8bc4\u4f30\u8868\uff0c\u7b80\u5355\u5c55\u793a\u8fc7\u6ee4\u524d\u540e\u6570\u636e\u603b\u4f53\u60c5\u51b5\u5982\u4e0b
\nless 01_clean\/Basic_Statistics_of_Sequencing_Quality.txt<\/p>\n

<\/p>\n

\u5927\u5bb6\u4e5f\u53ef\u4ee5\u628a\u6570\u636e\u4e0b\u8f7d\u5230\u672c\u5730\u8fdb\u884c\u67e5\u770b\uff0c\u53ef\u572801_clean\u8def\u5f84\u4e0b\u627e\u5230”Basic_Statistics_of_Sequencing_Quality.txt”\u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u63d0\u4f9b\u4e86\u8fc7\u6ee4\u524d\u540e\u6570\u636e\u8d28\u91cf\u7684\u5bf9\u6bd4\u7edf\u8ba1\u4fe1\u606f\uff0c\u53ef\u4ee5\u67e5\u770b\u4ee5\u4e0b\u6307\u6807\uff1a\u6570\u636e\u603b\u6570\u3001\u603b\u78b1\u57fa\u6570\u3001GC\u542b\u91cf\u3001Q20\u548cQ30\u7684\u6bd4\u4f8b\u7b49\uff0c\u53ef\u901a\u8fc7\u67e5\u770b\u8be5\u6587\u4ef6\u4e86\u89e3\u6570\u636e\u8d28\u91cf\u4e0e \u8fc7\u6ee4\u60c5\u51b5\uff0c\u622a\u56fe\u5982\u4e0b<\/p>\n

<\/p>\n

\u6839\u636e\u5b9e\u9a8c\u7ed3\u679c\u622a\u56fe\uff0c\u53ef\u4ee5\u5f97\u5230\u4ee5\u4e0b\u4fe1\u606f\uff1a<\/p>\n

\u603breads\u6570\u91cf\u4e3a471522\uff0c\u5176\u4e2d\u88ab\u8fc7\u6ee4\u7684reads\u6570\u91cf\u4e3a15497\uff0c\u5360\u603breads\u76843.29%\u3002 \u603b\u78b1\u57fa\u6570\u91cf\u4e3a23576100\uff0c\u88ab\u8fc7\u6ee4\u7684\u78b1\u57fa\u6570\u91cf\u4e3a774850 \uff0c\u5360\u603b\u78b1\u57fa\u76843.29%\u3002<\/p>\n

\u7ecf\u8fc7\u7b5b\u9009\u8fc7\u540e\u7684\u6570\u636e\u5982\u4e0b\uff1a<\/p>\n

\u78b1\u57faA\u7684\u6570\u91cf\u4e3a6425115\uff0c\u5360\u603b\u78b1\u57fa\u768428.18%\u3002 \u78b1\u57faC\u7684\u6570\u91cf\u4e3a2977487\uff0c\u5360\u603b\u78b1\u57fa\u768427.04%\u3002 \u78b1\u57faG\u7684\u6570\u91cf\u4e3a5497530\uff0c\u5360\u603b\u78b1\u57fa\u768424.11%\u3002 \u78b1\u57faT\u7684\u6570\u91cf\u4e3a5325587\uff0c\u5360\u603b\u78b1\u57fa\u768423.36%\u3002<\/p>\n

Q20\u8d28\u91cf\u503c\u7684reads\u6570\u91cf\u4e3a22701850\uff0c\u5360\u603breads\u768499.56%\u3002 Q30\u8d28\u91cf\u503c\u7684reads\u6570\u91cf\u4e3a22593121\uff0c\u5360\u603breads\u768499.09%\u3002<\/p>\n

\u4ee5\u4e0a\u7ed3\u679c\u663e\u793a\uff0c\u5728\u5b9e\u9a8c\u8fc7\u7a0b\u4e2d\u91c7\u53d6\u4e86\u6709\u6548\u7684\u8d28\u91cf\u63a7\u5236\u6b65\u9aa4\uff0cSOAPnuke filter\u5de5\u5177\u8fc7\u6ee4\u6389\u4e86\u8d28\u91cf\u8f83\u5dee\u7684reads \u548c\u78b1\u57fa\uff0c\u4ece\u800c\u63d0\u9ad8\u4e86\u5b9e\u9a8c\u6570\u636e\u7684\u8d28\u91cf\uff0c\u4ee5\u4fbf\u8fdb\u884c\u8fdb\u4e00\u6b65\u7684\u5206\u6790\uff0c\u6316\u6398\u5176\u4e2d\u7684\u751f\u7269\u4fe1\u606f\u5b66\u7279\u5f81\u3002<\/p>\n

\u53e6\u5916\uff0cFASTQC\u5de5\u5177\u8fd8\u751f\u6210\u4e86\u4e00\u4efd\u78b1\u57fa\u8d28\u91cf\u503c\u5206\u5e03\u56fe\u62a5\u544a\uff0c\u6253\u5f00FASTQC\u5de5\u5177\u751f\u6210\u7684\u78b1\u57fa\u8d28\u91cf\u503c\u5206\u5e03\u56fe\uff0c\u53ef\u4ee5\u6e05\u6670\u76f4\u89c2\u5730\u89c2\u5bdf\u5230\u6bcf\u4e2a\u78b1\u57fa\u4f4d\u7f6e\u4e0a\u7684\u8d28\u91cf\u503c\u60c5\u51b5\uff1a<\/p>\n

<\/p>\n

Per base sequence quality\u8bf4\u660e\uff1a\u5404\u4f4d\u7f6e\u78b1\u57fa\u8d28\u91cf\uff0c\u6bcf\u4e2aread\u5404\u4f4d\u7f6e\u78b1\u57fa\u7684\u6d4b\u5e8f\u8d28\u91cf\u3002\u6a2a\u8f74\u78b1\u57fa\u7684\u4f4d\u7f6e\uff0c\u7eb5\u8f74\u662f\u8d28\u91cf\u5206\u6570\uff0cQuality score=-10log10p\uff08p\u4ee3\u8868\u9519\u8bef\u7387\uff09\uff0c\u6240\u4ee5\u5f53\u8d28\u91cf\u5206\u6570\u4e3a40\u7684\u65f6\u5019\uff0cp\u5c31\u662f0.0001\uff0c\u4ee3\u8868\u8d28\u91cf\u5f88\u9ad8\u3002\u7ea2\u8272\u7ebf\u4ee3\u8868\u4e2d\u4f4d\u6570\uff0c\u84dd\u8272\u4ee3\u8868\u5e73\u5747\u6570\uff0c\u9ec4\u8272\u662f25%-75%\u533a\u95f4\uff0c\u89e6\u987b\u662f10%-90%\u533a\u95f4\u3002\u82e5\u4efb\u4e00\u4f4d\u7f6e\u7684\u4e0b\u56db\u5206\u4f4d\u6570\u4f4e\u4e8e10\u6216\u8005\u4e2d\u4f4d\u6570\u4f4e\u4e8e25\uff0c\u51fa\u73b0\u201c\u8b66\u544a\u201d\uff1b\u82e5\u4efb\u4e00\u4f4d\u7f6e\u7684\u4e0b\u56db\u5206\u4f4d\u6570\u4f4e\u4e8e5\u6216\u8005\u4e2d\u4f4d\u6570\u4f4e\u4e8e20\uff0c\u51fa\u73b0\u201c\u5931\u8d25\uff0cFail\u201d\u3002<\/p>\n

<\/p>\n

Per sequence quality scores\u8bf4\u660e\uff1a\u6a2a\u8f74\u4e3aquality\uff0c\u7eb5\u8f74\u4e3areads\u8ba1\u6570\u3002<\/p>\n

\u53ef\u4ee5\u770b\u51fa\uff0c\u5c0f\u679c\u7684\u6570\u636e\u7684\u8d28\u91cf\u6bd4\u8f83\u9ad8\uff0c\u8d28\u91cf\u5206\u6570\u572839\u4ee5\u4e0a\u3002<\/p>\n

<\/p>\n

Per base sequence content\u8bf4\u660e\uff1a\u78b1\u57fa\u5206\u5e03\uff0c\u5bf9\u6240\u6709reads\u7684\u6bcf\u4e00\u4e2a\u4f4d\u7f6e\uff0c\u7edf\u8ba1ATCG\u56db\u79cd\u78b1\u57fa\u7684\u5206\u5e03\uff0c\u6a2a\u8f74\u4e3a\u4f4d\u7f6e\uff0c\u7eb5\u8f74\u4e3a\u78b1\u57fa\u542b\u91cf\uff0c\u6b63\u5e38\u60c5\u51b5\u4e0b\u6bcf\u4e2a\u4f4d\u7f6e\u6bcf\u79cd\u78b1\u57fa\u51fa\u73b0\u7684\u6982\u7387\u662f\u76f8\u8fd1\u7684\uff0c\u56db\u6761\u7ebf\u5e94\u8be5\u5e73\u884c\u4e14\u76f8\u8fd1\u3002\u5f53\u90e8\u5206\u4f4d\u7f6e\u78b1\u57fa\u7684\u6bd4\u4f8b\u51fa\u73b0bias\u65f6\uff0c\u5373\u56db\u6761\u7ebf\u5728\u67d0\u4e9b\u4f4d\u7f6e\u7eb7\u4e71\u4ea4\u7ec7\uff0c\u5f80\u5f80\u63d0\u793a\u6211\u4eec\u6709overrepresented sequence\u7684\u6c61\u67d3\u3002\u672c\u7ed3\u679c\u6bcf\u79cd\u78b1\u57fa\u9891\u7387\u6709\u660e\u663e\u7684\u5dee\u522b\uff0c\u8bf4\u660e\u6709\u6c61\u67d3\u3002\u5f53\u4efb\u4e00\u4f4d\u7f6e\u7684A\/T\u6bd4\u4f8b\u4e0eG\/C\u6bd4\u4f8b\u76f8\u5dee\u8d85\u8fc710%\uff0c\u62a5’WARN’\uff1b\u5f53\u4efb\u4e00\u4f4d\u7f6e\u7684A\/T\u6bd4\u4f8b\u4e0eG\/C\u6bd4\u4f8b\u76f8\u5dee\u8d85\u8fc720%\uff0c\u62a5’FAIL’\u3002<\/p>\n

<\/p>\n

per sequence GC content\u8bf4\u660e\uff1a\u6a2a\u8f74\u4e3aGC\u542b\u91cf\uff0c\u7eb5\u8f74\u4e3aread\u8ba1\u6570\u3002\u7ea2\u8272\u4e3a\u5b9e\u9645\u6d4b\u5f97\uff0c\u84dd\u8272\u4e3a\u7406\u8bba\u5206\u5e03\u3002 \u504f\u79bb\u5927\u4e8e15%\uff0c\u62a5WARN\uff1b\u5927\u4e8e30%\uff0c\u62a5FAIL\u3002 \u8fd9\u91cc\u4e0e\u6807\u51c6\u66f2\u7ebf\u504f\u79bb\u8f83\u4e25\u91cd\uff0c\u5c0f\u679c\u7ecf\u8fc7\u67e5\u9605\u8d44\u6599\u5f97\u77e5\uff0c\u5982\u679c\u66f2\u7ebf\u5f62\u72b6\u4e0d\u7b26\uff0c\u4ee3\u8868\u6587\u5e93\u6c61\u67d3\u3002<\/p>\n

<\/p>\n

per base N content\u8bf4\u660e\uff1aN \u4ee3\u8868\u6d4b\u5e8f\u4eea\u4e0d\u80fd\u8bc6\u522b\u7684\u78b1\u57fa\uff0c\u6a2a\u8f74\u4ee3\u8868read\u4f4d\u7f6e\uff0c\u7eb5\u8f74\u4ee3\u8868\u5360\u6bd4\u3002\u5982\u679c\u6b63\u5e38\u6d4b\u5e8f\uff0c\u7ea2\u7ebf\u5e94\u8be5\u662f\u8d8b\u8fd1\u4e0e0\u7684\u76f4\u7ebf\u3002\u5f53\u4efb\u610f\u4f4d\u7f6eN\u5360\u6bd4\u5927\u4e8e5%\uff0c\u62a5WARN\uff1b\u5927\u4e8e20%\uff0c\u62a5FAIL\u3002\u8fd9\u91cc\u6d4b\u5e8f\u8d28\u91cf\u6ca1\u6709\u95ee\u9898\u3002<\/p>\n

<\/p>\n

\u957f\u5ea6\u4e00\u81f4\uff0c\u6ca1\u6709\u95ee\u9898\u3002<\/p>\n

<\/p>\n

sequence duplication levels\u8bf4\u660e\uff1a\u6a2a\u5750\u6807\u4e3a\u91cd\u590d\uff08duplication\uff09\u7684\u6b21\u6570\uff0c\u7eb5\u5750\u6807\u4e3areads\u7684\u6570\u76ee\uff0c\u4ee5unique reads\u7684\u603b\u6570\u4f5c\u4e3a100%\u3002\u8fd9\u91cc\u53ef\u80fd\u610f\u5473\u7740\u5b58\u5728\u67d0\u79cd\u6280\u672f\u95ee\u9898\uff0c\u5982PCR\u504f\u501a\u3001\u6587\u5e93\u6784\u5efa\u95ee\u9898\u6216\u8005\u6c61\u67d3\u7b49\u3002<\/p>\n

<\/p>\n

Kmer Content\u8bf4\u660e\uff1aKmer\u662f\u6307\u8fde\u7eed\u7684\u957f\u5ea6\u4e3ak\u7684\u6838\u82f7\u9178\u5e8f\u5217\u7247\u6bb5\uff0c\u901a\u8fc7\u8ba1\u7b97\u548c\u6bd4\u8f83\u8fd9\u4e9b\u7247\u6bb5\u7684\u9891\u7387\uff0c\u53ef\u4ee5\u4e86\u89e3\u6837\u672c\u4e2d\u4e0d\u540c\u6838\u82f7\u9178\u7684\u76f8\u5bf9\u4e30\u5ea6\u3002\u5728FastQC\u7684Kmer Content\u6a21\u5757\u4e2d\uff0c\u901a\u5e38\u4f1a\u663e\u793a\u5404\u4e2aKmer\u957f\u5ea6\uff08\u4f8b\u5982\uff0c4\u30015\u30016\u7b49\uff09\u7684\u9891\u7387\u5206\u5e03\u56fe\u3002\u6bcf\u4e2aKmer\u957f\u5ea6\u4ee3\u8868\u4e86\u4e0d\u540c\u957f\u5ea6\u7684\u6838\u82f7\u9178\u5e8f\u5217\u7247\u6bb5\u3002\u5206\u6790\u8fd9\u4e9b\u7247\u6bb5\u7684\u9891\u7387\u5206\u5e03\u53ef\u4ee5\u5f97\u5230\u6837\u672c\u4e2d\u5404\u79cd\u6838\u82f7\u9178\u7ec4\u6210\u7684\u76f8\u5bf9\u6bd4\u4f8b\u3002\u8fd9\u91cc\u7684kmer\u5206\u5e03\u6709\u5f02\u5e38\u51fa\u73b0\uff0c\u53ef\u80fd\u662f\u6709\u6c61\u67d3\u7684\u95ee\u9898\u3002<\/p>\n

\u672c\u6b21\u7684\u5206\u4eab\u5230\u8fd9\u91cc\u5c31\u7ed3\u675f\u5566\uff0c\u600e\u4e48\u6837\uff0c\u8d28\u91cf\u8bc4\u4f30\u7684\u64cd\u4f5c\u90e8\u5206\u662f\u4e0d\u662f\u5f88\u7b80\u5355\uff0c\u800c\u89c2\u770b\u7ed3\u679c\u7684\u90e8\u5206\u662f\u4e0d\u662f\u5e72\u8d27\u6ee1\u6ee1\u5462\uff1f\u76f8\u4fe1\u5c0f\u4f19\u4f34\u4eec\u4e5f\u90fd\u662f\u6536\u83b7\u6ee1\u6ee1\u5427\u3002\u751f\u4fe1\u5206\u6790\u7ecf\u5e38\u662f\u8fd9\u6837\uff0c\u64cd\u4f5c\u5f88\u7b80\u5355\u800c\u5206\u6790\u4e4d\u4e00\u770b\u6bd4\u8f83\u590d\u6742\uff0c\u4f46\u5b66\u4e60\u540e\u4e5f\u4f1a\u53d1\u73b0\u5176\u5b9e\u53ea\u662f\u201c\u7eb8\u8001\u864e\u201d\uff0c\u53ea\u8981\u5c0f\u4f19\u4f34\u4eec\u80af\u8ba4\u771f\u94bb\u7814\u5176\u5b9e\u4e5f\u662f\u5f88\u7b80\u5355\u7684\u3002<\/p>\n

\u5982\u679c\u5c0f\u4f19\u4f34\u4eec\u5e73\u65f6\u5728\u751f\u4fe1\u5206\u6790\u7684\u64cd\u4f5c\u8fc7\u7a0b\u4e2d\u9047\u5230\u56f0\u96be\uff0c\u6b22\u8fce\u5927\u5bb6\u4f7f\u7528\u5c0f\u679c\u5f00\u53d1\u7684\u751f\u4fe1\u5de5\u5177\u5e73\u53f0http:\/\/www.biocloudservice.com\/home.html<\/a>\uff0c\u5927\u5bb6\u5728\u65b0\u63a5\u89e6\u4e00\u4e2a\u77e5\u8bc6\u7684\u65f6\u5019\uff0c\u4e0e\u5176\u5148\u82b1\u8d39\u5927\u91cf\u65f6\u95f4\u6b7b\u5543\u77e5\u8bc6\u70b9\uff0c\u4e0d\u5982\u5148\u5229\u7528\u597d\u5de5\u5177\u5148\u81ea\u5df1\u4e0a\u624b\u63a5\u89e6\u6d41\u7a0b\uff0c\u5728\u8dd1\u5b8c\u4e00\u904d\u5168\u6d41\u7a0b\u540e\u518d\u8fd4\u56de\u53bb\u7406\u89e3\u77e5\u8bc6\u70b9\uff0c\u76f8\u4fe1\u53ef\u4ee5\u66f4\u597d\u66f4\u5feb\u5730\u7406\u89e3\uff0c\u8fbe\u5230\u4e8b\u534a\u529f\u500d\u7684\u6548\u679c\uff01<\/p>\n

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