{"id":70014,"date":"2026-11-14T22:16:43","date_gmt":"2026-11-14T14:16:43","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70014"},"modified":"2026-11-14T22:16:43","modified_gmt":"2026-11-14T14:16:43","slug":"fastp-paired-ends-orphans-read-count-denominators","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/fastp-paired-ends-orphans-read-count-denominators\/","title":{"rendered":"fastp \u62a5\u544a\u4fdd\u7559\u4e86\u4e8c\u5341\u56db\u6761 reads\uff0c\u4e3a\u4ec0\u4e48\u8f93\u51fa\u6587\u4ef6\u91cc\u80fd\u627e\u56de\u4e09\u5341\u4e00\u6761\uff1f"},"content":{"rendered":"
\n

\u62ff\u5230\u4e00\u5bf9\u53cc\u7aef FASTQ\uff0c\u7528 fastp \u8fc7\u6ee4\uff0c\u62a5\u544a\u663e\u793a\u8f93\u5165\u56db\u5341\u6761\u3001\u8fc7\u6ee4\u540e\u4e8c\u5341\u56db\u6761\u3002\u82e5\u6709\u4eba\u4ece\u8f93\u51fa\u76ee\u5f55\u4e2d\u6570\u5230\u4e09\u5341\u4e00\u6761\uff0c\u4ed6\u548c\u62a5\u544a\u4e00\u5b9a\u6709\u4e00\u4e2a\u6570\u9519\u4e86\u5417\uff1f\u6211\u4eec\u5236\u4f5c\u4e86\u4e8c\u5341\u5bf9\u540d\u5b57\u53ef\u8ffd\u6eaf\u7684\u8bfb\u6bb5\uff0c\u5206\u522b\u653e\u5165\u53cc\u7aef\u5747\u5408\u683c\u3001\u53ea\u6709\u5de6\u7aef\u5931\u8d25\u3001\u53ea\u6709\u53f3\u7aef\u5931\u8d25\u548c\u53cc\u7aef\u90fd\u5931\u8d25\u7684\u4f8b\u5b50\u3002\u8fd0\u884c\u540c\u4e00\u5957\u8fc7\u6ee4\u6761\u4ef6\u540e\uff0c\u53ea\u6539\u53d8\u662f\u5426\u4fdd\u5b58\u5408\u683c\u7684\u5b64\u7acb\u7aef\uff0c\u7ed3\u679c\u8fd9\u4e24\u4e2a\u6570\u5b57\u53ef\u4ee5\u540c\u65f6\u6210\u7acb\u3002\u8fd9\u4e2a\u7ec3\u4e60\u80fd\u5e2e\u8bfb\u8005\u5728\u9001\u5165\u6bd4\u5bf9\u524d\u8bf4\u6e05\u695a\u81ea\u5df1\u4fdd\u5b58\u4e86\u591a\u5c11\u5bf9\u3001\u53e6\u5916\u4fdd\u7559\u591a\u5c11\u5355\u7aef\uff0c\u4ee5\u53ca\u8868\u91cc\u7684\u767e\u5206\u6bd4\u7528\u4e86\u4ec0\u4e48\u5206\u6bcd\u3002<\/p>\n

\u53cc\u7aef\u6d4b\u5e8f\u81f3\u5c11\u6709\u4e09\u79cd\u8ba1\u6570\u5355\u4f4d<\/h2>\n

\u4e00\u4efd\u6765\u81ea\u540c\u4e00\u7247\u6bb5\u4e24\u7aef\u7684\u6d4b\u5e8f\u8bb0\u5f55\uff0c\u5728 R1 \u6587\u4ef6\u548c R2 \u6587\u4ef6\u5404\u5360\u4e00\u6761\u3002\u82e5\u6309\u7269\u7406\u7247\u6bb5\u6570\uff0c\u5b83\u662f\u4e00\u5bf9\u3002\u82e5\u6309 FASTQ \u8bb0\u5f55\u6570\uff0c\u5219\u662f\u4e24\u6761\u3002\u8d28\u63a7\u80fd\u5355\u72ec\u5224\u65ad\u67d0\u4e00\u7aef\u7684\u78b1\u57fa\u8d28\u91cf\u3001\u672a\u77e5\u78b1\u57fa\u6570\u548c\u957f\u5ea6\u662f\u5426\u5408\u683c\uff0c\u4f46\u5199\u5165\u5e38\u89c4\u914d\u5bf9\u8f93\u51fa\u65f6\uff0c\u4e24\u7aef\u8fd8\u8981\u80fd\u4f5c\u4e3a\u4e00\u5bf9\u5171\u540c\u4fdd\u7559\u3002\u4e8e\u662f\u201c\u901a\u8fc7\u5355\u7aef\u6761\u4ef6\u7684\u8bfb\u6bb5\u201d\u201c\u4f5c\u4e3a\u5b8c\u6574\u914d\u5bf9\u7559\u4e0b\u7684\u8bb0\u5f55\u201d\u548c\u201c\u5b9e\u9645\u5199\u8fdb\u6240\u6709\u6587\u4ef6\u7684\u8bb0\u5f55\u201d\u662f\u4e09\u79cd\u91cf\u3002\u5148\u7ed9\u6570\u5b57\u8865\u4e0a\u5355\u4f4d\uff0c\u518d\u5bf9\u7167\u4e0b\u6e38\u5de5\u5177\u8981\u6c42\u7684\u8f93\u5165\u5f62\u5f0f\uff0c\u6bd4\u62ff\u4e24\u4e2a\u767e\u5206\u6bd4\u76f4\u63a5\u76f8\u51cf\u66f4\u6709\u6548\u3002fastp \u4f5c\u8005\u8bf4\u660e\u53ca\u53cc\u7aef\u8f93\u51fa\u53c2\u6570<\/a><\/p>\n

\u4e00\u4e2a\u5b9e\u7528\u7ea6\u5b9a\u662f\u4e3a\u6bcf\u4e2a\u6837\u672c\u5efa\u7acb\u5c3a\u5bf8\u6700\u591a\u53ea\u6709\u51e0\u884c\u7684\u6536\u652f\u8868\u3002\u5217\u51fa\u539f\u59cb\u914d\u5bf9\u6570\u3001\u4e24\u7aef\u90fd\u5408\u683c\u7684\u914d\u5bf9\u6570\u3001\u53ea\u6709\u7b2c\u4e00\u7aef\u53ef\u7528\u7684\u6570\u3001\u53ea\u6709\u7b2c\u4e8c\u7aef\u53ef\u7528\u7684\u6570\u3001\u53cc\u7aef\u5747\u4e0d\u53ef\u7528\u7684\u6570\u3002\u672b\u5c3e\u8bb0\u5f55\u662f\u5426\u5b9e\u9645\u5199\u51fa\u8fd9\u4e24\u7c7b\u5b64\u7acb\u7aef\u3002\u5982\u679c\u6587\u4ef6\u91cc\u51fa\u73b0\u770b\u4f3c\u5c11\u4e00\u534a\u7684\u6570\u5b57\uff0c\u5148\u770b\u5bf9\u65b9\u662f\u62a5\u914d\u5bf9\u8fd8\u662f\u62a5\u7aef\u6570\u3002\u5982\u679c\u5b64\u7acb\u7aef\u5df2\u7ecf\u53e6\u5b58\uff0c\u5374\u4ecd\u628a\u5b83\u4eec\u5f3a\u884c\u4e0e\u53e6\u4e00\u4e2a\u65b9\u5411\u7684\u5b64\u7acb\u7aef\u9010\u884c\u62fc\u8d77\u6765\uff0c\u539f\u672c\u4e0d\u540c\u7247\u6bb5\u7684\u4e24\u6761\u8bfb\u6bb5\u4f1a\u88ab\u5047\u88c5\u6210\u540c\u4e00\u5bf9\uff0c\u6c61\u67d3\u7247\u6bb5\u957f\u5ea6\u3001\u65b9\u5411\u4e0e\u914d\u5bf9\u6bd4\u5bf9\u7ed3\u679c\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u8ba9\u5931\u8d25\u539f\u56e0\u4e00\u5f00\u59cb\u5c31\u5199\u5728\u8bfb\u6bb5\u540d\u5b57\u91cc<\/h2>\n

\u5728 Ubuntu \u5b89\u88c5 fastp 0.23.4\uff0c\u56fa\u5b9a\u968f\u673a\u79cd\u5b50\u751f\u6210\u4e8c\u5341\u5bf9\u957f\u5ea6\u5747\u4e3a\u4e03\u5341\u4e2a\u78b1\u57fa\u7684 FASTQ\u3002\u5341\u4e8c\u5bf9\u4e24\u7aef\u5747\u9ad8\u8d28\u91cf\uff0c\u56db\u5bf9\u4ec5\u7b2c\u4e8c\u7aef\u5168\u4e3a\u4f4e\u8d28\u91cf\uff0c\u4e09\u5bf9\u4ec5\u7b2c\u4e00\u7aef\u6709\u5341\u4e8c\u4e2a\u672a\u77e5\u78b1\u57fa\uff0c\u6700\u540e\u4e00\u5bf9\u4e24\u7aef\u5168\u4e3a\u4f4e\u8d28\u91cf\u3002\u5176\u4f59\u5e8f\u5217\u968f\u673a\u751f\u6210\uff0c\u8d28\u91cf\u5408\u683c\u7684\u78b1\u57fa\u7528\u9ad8\u8d28\u91cf\u5b57\u7b26\u8868\u793a\u3002\u4e3a\u8fd9\u4e2a\u4e13\u95e8\u68c0\u9a8c\u914d\u5bf9\u5173\u7cfb\u7684\u4f8b\u5b50\uff0c\u6211\u4eec\u5173\u95ed\u63a5\u5934\u4fee\u526a\u3001\u591a\u805a\u9e1f\u560c\u5464\u4fee\u526a\u548c\u91cd\u590d\u7387\u4f30\u8ba1\u3002\u8bbe\u5408\u683c\u8d28\u91cf\u9608\u503c\u4e3a\u4e8c\u5341\uff0c\u5141\u8bb8\u4e0d\u5408\u683c\u78b1\u57fa\u6700\u591a\u5360\u56db\u5206\u4e4b\u4e00\uff0c\u672a\u77e5\u78b1\u57fa\u6570\u4e0a\u9650\u4e3a\u4e94\uff0c\u6700\u77ed\u957f\u5ea6\u4e3a\u4e8c\u5341\u4e94\u3002\u6240\u6709\u8bfb\u6bb5\u7684\u540d\u5b57\u5e26\u6709\u53ef\u6838\u67e5\u7684\u7f16\u53f7\u548c\u9884\u8bbe\u573a\u666f\u3002<\/p>\n

\u5148\u53ea\u8f93\u51fa\u5e38\u89c4 R1 \u548c R2\u3002\u4e24\u4e2a\u6587\u4ef6\u5404\u6709\u5341\u4e8c\u6761\uff0c\u540d\u5b57\u5339\u914d\uff0c\u6070\u597d\u662f\u90a3\u5341\u4e8c\u5bf9\u53cc\u7aef\u90fd\u5408\u683c\u7684\u8bfb\u6bb5\u3002\u518d\u7528\u76f8\u540c\u8f93\u5165\u548c\u7b5b\u9009\u53c2\u6570\uff0c\u53e6\u5916\u6307\u5b9a\u4e24\u4e2a\u5b64\u7acb\u7aef\u8f93\u51fa\u6587\u4ef6\u3002\u5e38\u89c4\u914d\u5bf9\u6587\u4ef6\u4ecd\u5404\u6709\u5341\u4e8c\u6761\u3002\u7b2c\u4e00\u7aef\u5b64\u7acb\u6587\u4ef6\u53e6\u5916\u6709\u56db\u6761\uff0c\u6765\u81ea\u539f\u6765\u7b2c\u4e8c\u7aef\u8d28\u91cf\u592a\u4f4e\u7684\u56db\u4e2a\u7247\u6bb5\u3002\u7b2c\u4e8c\u7aef\u5b64\u7acb\u6587\u4ef6\u6709\u4e09\u6761\uff0c\u6765\u81ea\u539f\u6765\u7b2c\u4e00\u7aef\u672a\u77e5\u78b1\u57fa\u8d85\u9650\u7684\u4e09\u4e2a\u7247\u6bb5\u3002\u5404\u6587\u4ef6\u4e2d\u7684\u8bfb\u6bb5\u6807\u8bc6\u90fd\u9010\u6761\u5bf9\u8fc7\uff0c\u53cc\u7aef\u5747\u5931\u8d25\u7684\u6700\u540e\u4e00\u5bf9\u6ca1\u6709\u8fdb\u5165\u4efb\u4f55\u5408\u683c\u8f93\u51fa\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n\n
\u672c\u6b21\u5b9e\u9645\u6838\u5bf9\u7684\u91cf<\/th>\n\u53ea\u4fdd\u5b58\u5e38\u89c4\u914d\u5bf9<\/th>\n\u53e6\u5b58\u5408\u683c\u5b64\u7acb\u7aef<\/th>\n<\/tr>\n<\/thead>\n
\u5b8c\u6574\u914d\u5bf9\u6570<\/td>\n12 \u5bf9<\/td>\n12 \u5bf9<\/td>\n<\/tr>\n
\u5e38\u89c4\u914d\u5bf9\u6587\u4ef6\u5408\u8ba1<\/td>\n24 \u6761<\/td>\n24 \u6761<\/td>\n<\/tr>\n
\u7b2c\u4e00\u7aef \/ \u7b2c\u4e8c\u7aef\u5b64\u7acb\u8bb0\u5f55<\/td>\n0 \/ 0 \u6761\u5199\u51fa<\/td>\n4 \/ 3 \u6761\u5199\u51fa<\/td>\n<\/tr>\n
\u6240\u6709\u5408\u683c\u8f93\u51fa\u6587\u4ef6\u5408\u8ba1<\/td>\n24 \u6761<\/td>\n31 \u6761<\/td>\n<\/tr>\n
\u62a5\u544a\u4e2d after_filtering \u7684\u603b\u8bfb\u6bb5\u6570<\/td>\n24<\/td>\n24<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u62a5\u544a\u6709
20 \u5bf9\u6a21\u62df\u8bfb\u6bb5\uff5c\u624b\u5de5\u8bbe\u7f6e\u7aef\u522b\u4e0e\u5931\u8d25\u539f\u56e0\uff0c\u518d\u9010\u6761\u6838\u5bf9\u8f93\u51fa\u3002<\/figcaption><\/figure>\n

\u8fd9\u4e2a\u8f93\u51fa\u63ed\u793a\u4e86\u53e6\u4e00\u4e2a\u5bb9\u6613\u6df7\u6dc6\u7684\u6307\u6807\u3002\u4e24\u6b21\u62a5\u544a\u7684\u8fc7\u6ee4\u539f\u56e0\u6c47\u603b\u91cc\uff0c\u4f4e\u8d28\u91cf\u8bfb\u6bb5\u4e3a\u5341\uff0c\u672a\u77e5\u78b1\u57fa\u8d85\u9650\u4e3a\u516d\u3002\u6309\u6211\u4eec\u6784\u9020\u7684\u6570\u636e\uff0c\u771f\u6b63\u5168\u4f4e\u8d28\u91cf\u7684\u7aef\u53ea\u6709\u516d\u6761\uff0c\u5373\u56db\u4e2a\u574f\u7b2c\u4e8c\u7aef\u548c\u6700\u540e\u4e24\u4e2a\u574f\u7aef\u3002\u542b\u8fc7\u591a\u672a\u77e5\u78b1\u57fa\u7684\u7aef\u4e5f\u53ea\u6709\u4e09\u6761\u3002\u62a5\u544a\u4e2d\u7684\u5341\u548c\u516d\u5728\u672c\u4f8b\u91cc\u5206\u522b\u662f\u4e94\u4e2a\u53d7\u4f4e\u8d28\u91cf\u5f71\u54cd\u7684\u914d\u5bf9\u4e0e\u4e09\u4e2a\u53d7\u672a\u77e5\u78b1\u57fa\u5f71\u54cd\u7684\u914d\u5bf9\uff0c\u5404\u6309\u4e24\u6761\u8bb0\u5f55\u7d2f\u8ba1\u3002\u5b83\u4eec\u53ef\u4ee5\u4e0e\u4e8c\u5341\u56db\u6761\u914d\u5bf9\u5408\u683c\u7aef\u4e00\u8d77\u52a0\u5230\u56db\u5341\uff0c\u5374\u4e0d\u80fd\u636e\u6b64\u65ad\u8a00\u6709\u5341\u4e2a\u7269\u7406\u8bfb\u6bb5\u7684\u8d28\u91cf\u5b57\u7b26\u4e32\u672c\u8eab\u4e0d\u5408\u683c\u3002\u8981\u6392\u67e5\u7a76\u7adf\u662f\u54ea\u4e00\u7aef\u51fa\u9519\uff0c\u5e94\u5f53\u6838\u5bf9\u6765\u6e90\u8bfb\u6bb5\u548c\u5b64\u7acb\u7aef\u7684\u540d\u5b57\uff0c\u5e76\u67e5\u770b\u5355\u7aef\u8d28\u91cf\u5206\u5e03\u3002fastp \u7684\u914d\u5bf9\u5904\u7406\u5b9e\u73b0<\/a><\/p>\n

fastp -i source_R1.fastq -I source_R2.fastq -o paired_R1.fq -O paired_R2.fq \\\r\n  --unpaired1 solo_R1.fq --unpaired2 solo_R2.fq \\\r\n  --qualified_quality_phred 20 --unqualified_percent_limit 25 --n_base_limit 5 \\\r\n  --length_required 25 --disable_adapter_trimming --disable_trim_poly_g \\\r\n  --dont_eval_duplication --thread 1 -j result.json -h result.html\r\n<\/code><\/pre>\n
\u5728\u8fd9\u4e2a\u4f8b\u5b50\u4e2d\uff0c\u6309\u5b8c\u6574\u914d\u5bf9\u5224\u65ad\uff0c\u4fdd\u7559\u6bd4\u4f8b\u4e3a\u5341\u4e8c\u9664\u4ee5\u4e8c\u5341\uff0c\u5373\u516d\u6210\u3002\u82e5\u5206\u6790\u5141\u8bb8\u5229\u7528\u5408\u683c\u5b64\u7acb\u7aef\uff0c\u5b9e\u9645\u53ef\u4ea4\u7ed9\u540e\u7eed\u6b65\u9aa4\u7684\u8bb0\u5f55\u4e3a\u4e09\u5341\u4e00\u9664\u4ee5\u56db\u5341\uff0c\u5373\u767e\u5206\u4e4b\u4e03\u5341\u4e03\u70b9\u4e94\u3002\u5c06\u4e24\u79cd\u6bd4\u4f8b\u5e76\u6392\u5199\u51fa\u6765\uff0c\u540c\u65f6\u6807\u6e05\u662f\u5426\u542f\u7528\u5b64\u7acb\u7aef\u8f93\u51fa\uff0c\u5b9e\u9a8c\u540c\u4e8b\u5c31\u4e0d\u4f1a\u628a\u201c\u4fdd\u7559\u7387\u53d8\u9ad8\u201d\u8bef\u89e3\u6210\u8fc7\u6ee4\u9608\u503c\u5df2\u7ecf\u653e\u5bbd\u3002<\/p>\n
\u51b3\u5b9a\u4e0b\u6e38\u600e\u4e48\u63a5\uff0c\u6bd4\u628a\u6bcf\u4e00\u6761 read \u90fd\u7559\u4e0b\u66f4\u91cd\u8981<\/h2>\n
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