{"id":70085,"date":"2026-11-14T22:57:30","date_gmt":"2026-11-14T14:57:30","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70085"},"modified":"2026-11-14T22:57:30","modified_gmt":"2026-11-14T14:57:30","slug":"bowtie2-local-soft-clipping-read-coverage","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/bowtie2-local-soft-clipping-read-coverage\/","title":{"rendered":"Bowtie 2 \u5b9e\u8dd1\uff5c\u4e00\u6761 110 bp \u8bfb\u6bb5\u62a5\u4e86\u96f6\u9519\u914d\uff0c\u4e3a\u4ec0\u4e48\u5b9e\u9645\u53ea\u5bf9\u4e0a 73 bp\uff1f"},"content":{"rendered":"
\n

\u628a Bowtie 2 \u5207\u6362\u5230\u5c40\u90e8\u6bd4\u5bf9\u540e\uff0c\u6bd4\u5bf9\u7387\u4e0a\u5347\uff0c\u6709\u4e9b\u65b0\u627e\u5230\u7684\u8bfb\u6bb5\u751a\u81f3\u663e\u793a\u96f6\u9519\u914d\u3002\u5982\u679c\u8981\u5224\u65ad\u6837\u672c\u91cc\u6709\u6ca1\u6709\u67d0\u4e2a\u76ee\u6807\u5e8f\u5217\uff0c\u4ec5\u51ed\u8fd9\u4e24\u4e2a\u6307\u6807\u5f88\u5bb9\u6613\u9ad8\u4f30\u8bc1\u636e\u3002\u6211\u4eec\u5408\u6210\u4e86\u4e00\u6761\u4e00\u767e\u4e00\u5341\u78b1\u57fa\u7684\u5355\u7aef\u8bfb\u6bb5\uff0c\u4e2d\u95f4\u4e03\u5341\u4e2a\u78b1\u57fa\u9010\u4e2a\u53d6\u81ea\u53c2\u8003\uff0c\u4e24\u7aef\u5404\u52a0\u4e8c\u5341\u4e2a\u968f\u673a\u78b1\u57fa\u3002\u7aef\u5230\u7aef\u6a21\u5f0f\u5c06\u5b83\u6807\u4e3a\u672a\u6bd4\u5bf9\uff0c\u5c40\u90e8\u6a21\u5f0f\u627e\u5230\u4e03\u5341\u4e09\u4e2a\u543b\u5408\u78b1\u57fa\uff0c\u7f16\u8f91\u8ddd\u79bb\u4e3a\u96f6\u3002\u591a\u51fa\u6765\u7684\u4e09\u4f4d\u548c\u6d88\u5931\u7684\u4e09\u5341\u4e03\u4f4d\u90fd\u80fd\u4ece\u539f\u59cb\u5e8f\u5217\u89e3\u91ca\uff0c\u5f04\u6e05\u5b83\u4eec\u6bd4\u5355\u770b\u6bd4\u5bf9\u7387\u66f4\u6709\u7528\u3002<\/p>\n

\u4e24\u79cd\u6a21\u5f0f\u7a76\u7adf\u5141\u8bb8\u54ea\u4e00\u90e8\u5206\u8d21\u732e\u5f97\u5206<\/h2>\n

\u7aef\u5230\u7aef\u6a21\u5f0f\u8981\u6c42\u8bfb\u6bb5\u4ece\u4e00\u7aef\u5230\u53e6\u4e00\u7aef\u8fdb\u5165\u6bd4\u5bf9\uff0c\u5141\u8bb8\u6309\u8bc4\u5206\u89c4\u5219\u51fa\u73b0\u9519\u914d\u548c\u7f3a\u53e3\u3002\u82e5\u6700\u4f73\u5019\u9009\u4ecd\u8fbe\u4e0d\u5230\u6700\u4f4e\u5f97\u5206\uff0c\u5c31\u53ef\u80fd\u7559\u4e0b\u4e00\u6761\u672a\u6bd4\u5bf9\u8bb0\u5f55\u3002\u5c40\u90e8\u6a21\u5f0f\u5141\u8bb8\u5728\u7aef\u90e8\u8f6f\u526a\u5207\uff0c\u4ee5\u8bfb\u6bb5\u7684\u4e00\u6bb5\u4e0e\u53c2\u8003\u5bf9\u9f50\u3002\u88ab\u526a\u5207\u7684\u78b1\u57fa\u4ecd\u5728\u8f93\u51fa\u7684\u5e8f\u5217\u5b57\u6bb5\u91cc\uff0c\u53ef\u4ee5\u9010\u4e2a\u53d6\u56de\u68c0\u67e5\u3002\u5b83\u4eec\u4e0d\u5360\u53c2\u8003\u5750\u6807\uff0c\u4e5f\u4e0d\u8ba1\u5165\u76f8\u5e94\u5bf9\u9f50\u7247\u6bb5\u7684\u7f16\u8f91\u8ddd\u79bb\u3002\u9047\u5230\u4e00\u4e32\u8f6f\u526a\u5207\uff0c\u5148\u628a\u4e24\u7aef\u548c\u4e2d\u95f4\u753b\u5f00\uff0c\u518d\u95ee\u54ea\u4e00\u6bb5\u652f\u6301\u76ee\u6807\u5e8f\u5217\u3002Bowtie 2 \u5b98\u65b9\u624b\u518c\u4e2d\u7684\u6bd4\u5bf9\u6a21\u5f0f\u4e0e\u8bc4\u5206<\/a><\/p>\n

\u4e24\u79cd\u6a21\u5f0f\u7684\u6253\u5206\u4f53\u7cfb\u4e5f\u6709\u5dee\u5f02\u3002\u4f7f\u7528\u672c\u6b21\u7684\u9ed8\u8ba4\u8bc4\u5206\u65f6\uff0c\u7aef\u5230\u7aef\u6a21\u5f0f\u7684\u5b8c\u5168\u5339\u914d\u53ef\u5f97\u96f6\u5206\uff0c\u51fa\u73b0\u9519\u914d\u6216\u7f3a\u53e3\u4f1a\u53d7\u7f5a\u3002\u5c40\u90e8\u6a21\u5f0f\u6bcf\u4e2a\u5339\u914d\u78b1\u57fa\u6709\u6b63\u5411\u5956\u52b1\uff0c\u6700\u540e\u518d\u6309\u8bfb\u957f\u76f8\u5173\u7684\u6700\u4f4e\u5206\u8981\u6c42\u5224\u65ad\u662f\u5426\u62a5\u544a\u3002\u4e8e\u662f\u540c\u4e00\u6761\u5b8c\u7f8e\u8bfb\u6bb5\u7684\u5f97\u5206\u53ef\u4ee5\u5728\u4e24\u6b21\u8fd0\u884c\u4e2d\u4e00\u4e2a\u4e3a\u96f6\uff0c\u4e00\u4e2a\u4e3a\u4e24\u767e\u4e8c\u5341\u3002\u628a\u4e24\u5f20\u8f93\u51fa\u8868\u62fc\u5728\u4e00\u8d77\uff0c\u7136\u540e\u6309\u6bd4\u5bf9\u5f97\u5206\u4ece\u9ad8\u5230\u4f4e\u9009\u6700\u4f18\u6a21\u5f0f\uff0c\u4f1a\u628a\u8bc4\u5206\u5b9a\u4e49\u7684\u5dee\u5f02\u8bef\u8ba4\u4f5c\u751f\u7269\u5b66\u8bc1\u636e\u7684\u5dee\u5f02\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u4e03\u5341\u4e2a\u8bbe\u8ba1\u78b1\u57fa\u4e3a\u4ec0\u4e48\u62a5\u51fa\u4e03\u5341\u4e09\u4e2a<\/h2>\n

\u5b89\u88c5 Bowtie 2 2.5.2 \u540e\uff0c\u6211\u4eec\u4e3a\u4e00\u6761\u4e00\u5343\u516d\u767e\u78b1\u57fa\u7684\u5408\u6210\u5e8f\u5217\u5efa\u7acb\u7d22\u5f15\uff0c\u51c6\u5907\u4e09\u4e2a\u957f\u5ea6\u76f8\u540c\u7684\u67e5\u8be2\u3002\u7b2c\u4e00\u4e2a\u5b8c\u5168\u53d6\u81ea\u53c2\u8003\uff0c\u4f5c\u4e3a\u9633\u6027\u5bf9\u7167\u3002\u7b2c\u4e8c\u4e2a\u4fdd\u7559\u53c2\u8003\u6838\u5fc3\u3001\u4e24\u7aef\u6dfb\u52a0\u968f\u673a\u5e8f\u5217\u3002\u7b2c\u4e09\u4e2a\u5168\u90e8\u968f\u673a\u751f\u6210\uff0c\u7528\u6765\u68c0\u67e5\u5c40\u90e8\u6a21\u5f0f\u662f\u5426\u4f1a\u65e0\u6761\u4ef6\u7ed9\u4efb\u4f55\u8bfb\u6bb5\u5b89\u6392\u4f4d\u7f6e\u3002\u4e24\u6b21\u8fd0\u884c\u7528\u540c\u4e00\u4efd FASTQ\u3001\u540c\u4e00\u7d22\u5f15\u548c\u56fa\u5b9a\u7684\u968f\u673a\u79cd\u5b50\uff0c\u53ea\u6709\u6bd4\u5bf9\u6a21\u5f0f\u4e0d\u540c\u3002\u5355\u72ec\u4fdd\u7559\u4e24\u4efd SAM\uff0c\u53ef\u4ee5\u6309\u8bfb\u6bb5\u540d\u5e76\u6392\u68c0\u67e5\u3002<\/p>\n

\n\n\n\n\n\n\n\n
\u8bfb\u6bb5<\/th>\n\u7aef\u5230\u7aef\u6a21\u5f0f<\/th>\n\u5c40\u90e8\u6a21\u5f0f<\/th>\n<\/tr>\n<\/thead>\n
\u5168\u957f\u53d6\u81ea\u53c2\u8003<\/td>\n110M\uff0cAS 0\uff0cNM 0<\/td>\n110M\uff0cAS 220\uff0cNM 0<\/td>\n<\/tr>\n
70 bp \u6838\u5fc3\uff0c\u4e24\u7aef\u5404\u52a0 20 bp<\/td>\n\u672a\u6bd4\u5bf9\uff0cFLAG 4<\/td>\n20S73M17S\uff0cAS 146\uff0cNM 0<\/td>\n<\/tr>\n
110 bp \u5168\u90e8\u968f\u673a<\/td>\n\u672a\u6bd4\u5bf9<\/td>\n\u672a\u6bd4\u5bf9<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u96f6\u9519\u914d\uff0c\u8986\u76d6\u4e86\u591a\u5c11\u3002\u540c\u4e00\u6761
\u540c\u4e00\u6761 110 bp \u8bfb\u6bb5\u542b 70 bp \u53c2\u8003\u6838\u5fc3\uff0c\u4e24\u4fa7\u63a5\u5165\u968f\u673a\u5e8f\u5217\u3002<\/figcaption><\/figure>\n

\u5bf9\u4e8e\u7b2c\u4e8c\u6761\u8bfb\u6bb5\uff0c\u7a0b\u5e8f\u62a5\u544a\u53c2\u8003\u8d77\u70b9\u4e03\u767e\u4e00\u5341\u4e00\uff0c\u5148\u526a\u53bb\u5de6\u7aef\u4e8c\u5341\u4f4d\uff0c\u53f3\u7aef\u526a\u53bb\u5341\u4e03\u4f4d\u3002\u8bbe\u5b9a\u4e2d\u53f3\u7aef\u539f\u672c\u662f\u4e8c\u5341\u4e2a\u968f\u673a\u78b1\u57fa\uff0c\u5176\u4e2d\u524d\u4e09\u4e2a\u78b0\u5de7\u4e5f\u4e0e\u53c2\u8003\u76f8\u90bb\u4f4d\u7f6e\u76f8\u540c\uff0c\u5ef6\u957f\u6bd4\u5bf9\u53ef\u4ee5\u7ee7\u7eed\u5f97\u5206\u3002\u89c2\u5bdf\u5230\u7684\u8fb9\u754c\u7531\u5e8f\u5217\u548c\u8bc4\u5206\u51b3\u5b9a\uff0c\u8f6f\u4ef6\u5e76\u4e0d\u77e5\u9053\u5408\u6210\u65f6\u5728\u54ea\u4e2a\u4f4d\u7f6e\u8fde\u63a5\u4e86\u4e24\u6bb5\u3002\u5047\u5982\u8981\u5229\u7528\u8f6f\u526a\u5207\u5b9a\u4f4d\u63a5\u5934\u6216\u91cd\u6392\uff0c\u8fd9\u4e09\u4f4d\u5de7\u5408\u5c31\u8bf4\u660e\u4e86\u4e3a\u4ec0\u4e48\u64cd\u4f5c\u4e32\u7684\u8fb9\u754c\u672a\u5fc5\u7b49\u4e8e\u5206\u5b50\u4e8b\u4ef6\u7684\u7cbe\u786e\u65ad\u70b9\u3002\u6b64\u5904\u53ef\u4ee5\u9010\u78b1\u57fa\u6838\u67e5\uff0c\u662f\u56e0\u4e3a\u6211\u4eec\u77e5\u9053\u4eba\u5de5\u6784\u9020\u7684\u771f\u503c\u3002<\/p>\n

\u4e03\u5341\u4e09\u4e2a\u88ab\u5bf9\u9f50\u7684\u78b1\u57fa\u5360\u5168\u8bfb\u957f\u7ea6\u767e\u5206\u4e4b\u516d\u5341\u516d\u70b9\u56db\u3002\u5728\u8fd9\u4e2a\u8fde\u7eed\u5339\u914d\u7684\u4f8b\u5b50\u91cc\uff0c\u7f16\u8f91\u8ddd\u79bb\u4e3a\u96f6\u8bf4\u660e\u5bf9\u9f50\u90e8\u5206\u6ca1\u6709\u89c2\u5bdf\u5230\u5dee\u5f02\uff0c\u4f59\u4e0b\u4e09\u5341\u4e03\u4e2a\u78b1\u57fa\u6ca1\u6709\u7ed9\u76ee\u6807\u4f4d\u7f6e\u8d21\u732e\u543b\u5408\u8bc1\u636e\u3002\u8bfb\u771f\u5b9e\u64cd\u4f5c\u4e32\u65f6\uff0c\u53ea\u6709\u672c\u4f8b\u8fd9\u6837\u7684\u5355\u5757\u8fde\u7eed\u5339\u914d\u624d\u53ef\u4ee5\u76f4\u63a5\u62ff\u4e2d\u95f4\u4e00\u4e2a\u6570\u5b57\u4f5c\u5206\u5b50\u3002\u82e5\u51fa\u73b0\u63d2\u5165\u3001\u7f3a\u5931\u3001\u8df3\u8dc3\u6216\u591a\u4e2a\u5339\u914d\u5757\uff0c\u8981\u5148\u8bf4\u660e\u662f\u7edf\u8ba1\u67e5\u8be2\u4e0a\u5df2\u5bf9\u9f50\u7684\u6bd4\u4f8b\uff0c\u8fd8\u662f\u53c2\u8003\u4e0a\u8986\u76d6\u7684\u8de8\u5ea6\uff0c\u518d\u9010\u7c7b\u6c42\u548c\u3002\u628a\u7f3a\u5931\u7684\u53c2\u8003\u957f\u5ea6\u8ba1\u5165\u8bfb\u6bb5\u957f\u5ea6\u5c31\u4f1a\u5f97\u5230\u9519\u8bef\u6bd4\u4f8b\u3002SAM \u89c4\u8303\u4e2d\u7684\u64cd\u4f5c\u4e32\u4e0e\u5750\u6807\u6d88\u8017<\/a><\/p>\n

bowtie2-build ref.fa index\r\nbowtie2 --end-to-end -x index -U query.fq --seed 37 -S end.sam\r\nbowtie2 --local -x index -U query.fq --seed 37 -S local.sam\r\nawk -F '\\t' '$1=="tails" || $1=="perfect"' local.sam\r\n<\/code><\/pre>\n
\u672c\u6b21\u5b8c\u6574\u9633\u6027\u5bf9\u7167\u5728\u4e24\u4e2a\u6a21\u5f0f\u4e2d\u90fd\u662f\u4ece\u53c2\u8003\u7684\u7b2c\u516d\u767e\u4e5d\u5341\u4e00\u4f4d\u5f00\u59cb\uff0c\u5b8c\u5168\u968f\u673a\u7684\u67e5\u8be2\u5219\u4e24\u6b21\u90fd\u6ca1\u6709\u547d\u4e2d\u3002\u6b63\u8d1f\u5bf9\u7167\u5171\u540c\u8bf4\u660e\uff0c\u5728\u8fd9\u4efd\u7279\u5b9a\u7d22\u5f15\u4e0a\uff0c\u6539\u53d8\u6a21\u5f0f\u627e\u56de\u7684\u662f\u5e26\u6709\u5171\u4eab\u6838\u5fc3\u7684\u8bfb\u6bb5\u3002\u771f\u5b9e\u5b9e\u9a8c\u53ef\u4ee5\u7528\u5df2\u77e5\u5e8f\u5217\u7684\u52a0\u6807\u6837\u672c\u505a\u76f8\u4f3c\u6838\u67e5\uff0c\u518d\u89c2\u5bdf\u77ed\u5339\u914d\u662f\u5426\u96c6\u4e2d\u843d\u5728\u7279\u5b9a\u7684\u4f4e\u590d\u6742\u5ea6\u533a\u57df\u3002<\/p>\n
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