{"id":71507,"date":"2026-11-15T01:10:53","date_gmt":"2026-11-14T17:10:53","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71507"},"modified":"2026-11-15T01:15:15","modified_gmt":"2026-11-14T17:15:15","slug":"odgi-position-graph-path-inversion-offset-dna-check","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/odgi-position-graph-path-inversion-offset-dna-check\/","title":{"rendered":"ODGI \u5b9e\u8dd1\uff5c\u56fe\u4e0a\u7684\u4f4d\u7f6e\u80fd\u6295\u5230\u53e6\u4e00\u6761\u8def\u5f84\uff0c\u4e3a\u4ec0\u4e48\u8fd8\u8981\u7528 FASTA \u6838\u5bf9\u76ee\u6807\u78b1\u57fa\uff1f"},"content":{"rendered":"
\n

\u4e00\u6761\u6837\u672c\u8def\u5f84\u6bd4\u53c2\u8003\u591a\u51fa\u4e94\u4e2a\u78b1\u57fa\uff0c\u8fd8\u628a\u4e2d\u95f4\u4e00\u6bb5\u53cd\u5411\u653e\u7f6e\u3002\u73b0\u5728\u8981\u628a\u53c2\u8003\u4e0a\u7684\u4e00\u4e2a\u78b1\u57fa\u6295\u5230\u8fd9\u6761\u8def\u5f84\uff0c\u5e94\u8be5\u76f4\u63a5\u52a0\u4e94\u3001\u4ea4\u6362\u94fe\u65b9\u5411\uff0c\u8fd8\u662f\u5148\u627e\u8fd9\u6761\u78b1\u57fa\u6240\u5728\u7684\u56fe\u8282\u70b9\uff1f\u6211\u4eec\u7528 ODGI \u6784\u5efa\u4e00\u5f20\u53ef\u4ee5\u624b\u7b97\u7684\u5c0f\u56fe\uff0c\u5728\u5171\u4eab\u6b63\u5411\u7247\u6bb5\u3001\u5171\u4eab\u53cd\u5411\u7247\u6bb5\u548c\u6837\u672c\u72ec\u6709\u7247\u6bb5\u5206\u522b\u67e5\u8be2\u4f4d\u7f6e\uff0c\u518d\u4ece\u5de5\u5177\u5bfc\u51fa\u7684 FASTA \u9010\u78b1\u57fa\u6838\u5bf9\u3002\u4e09\u79cd\u4f4d\u7f6e\u90fd\u7ed9\u4e86\u76ee\u6807\u5750\u6807\uff0c\u4f46\u8fd9\u4e09\u4e2a\u6570\u5b57\u80fd\u652f\u6301\u7684\u89e3\u91ca\u4e0d\u540c\u3002ODGI \u4f4d\u7f6e\u8f6c\u6362\u8bf4\u660e<\/a><\/p>\n

\u5148\u628a\u4e24\u6761\u5b8c\u6574\u8def\u5f84\u62fc\u51fa\u6765<\/h2>\n

\u56fe\u4e2d\u6709\u56db\u4e2a\u8282\u70b9\uff0c\u957f\u5ea6\u5206\u522b\u4e3a\u5341\u3001\u5341\u4e8c\u3001\u516b\u3001\u4e94\u4e2a\u78b1\u57fa\u3002\u53c2\u8003\u8def\u5f84\u6309\u4e00\u3001\u4e8c\u3001\u4e09\u53f7\u8282\u70b9\u7684\u6b63\u5411\u987a\u5e8f\u7ecf\u8fc7\uff0c\u957f\u4e09\u5341\u78b1\u57fa\u3002\u53e6\u4e00\u6761\u8def\u5f84\u5148\u8d70\u4e00\u53f7\uff0c\u7136\u540e\u7a7f\u8fc7\u53c2\u8003\u91cc\u6ca1\u6709\u7684\u56db\u53f7\uff0c\u518d\u4ece\u53cd\u65b9\u5411\u8d70\u8fc7\u4e8c\u53f7\uff0c\u6700\u540e\u6b63\u5411\u901a\u8fc7\u4e09\u53f7\uff0c\u603b\u957f\u4e09\u5341\u4e94\u78b1\u57fa\u3002\u6211\u4eec\u628a\u8282\u70b9\u78b1\u57fa\u548c\u65b9\u5411\u5148\u5199\u5728\u7eb8\u9762\u4e0a\uff0c\u624b\u5de5\u751f\u6210\u4e24\u6761\u671f\u671b\u5e8f\u5217\uff0c\u7528\u5de5\u5177\u5bfc\u51fa\u7684\u4e24\u6761\u8def\u5f84\u9010\u5b57\u9a8c\u8bc1\u3002\u53ea\u6709\u8fd9\u4e00\u6b65\u6210\u7acb\uff0c\u540e\u9762\u53d1\u73b0\u7684\u5dee\u5f02\u624d\u53ef\u4ee5\u6cbf\u7740\u8282\u70b9\u3001\u4e0b\u6807\u3001\u65b9\u5411\u9010\u5c42\u5b9a\u4f4d\u3002ODGI \u9879\u76ee\u4e0e\u56fe\u64cd\u4f5c\u547d\u4ee4<\/a><\/p>\n

\u5bf9\u5355\u4e2a\u4f4d\u7f6e\u6709\u4e09\u79cd\u5e38\u89c1\u63cf\u8ff0\u3002\u7b2c\u4e00\u79cd\u662f\u201c\u5728\u54ea\u6761\u6837\u672c\u8def\u5f84\u7684\u54ea\u4e2a\u504f\u79fb\u201d\uff0c\u7b2c\u4e8c\u79cd\u662f\u201c\u5728\u54ea\u4e2a\u56fe\u8282\u70b9\u3001\u8282\u70b9\u5185\u54ea\u4e2a\u504f\u79fb\u3001\u4ee5\u54ea\u4e2a\u65b9\u5411\u7ecf\u8fc7\u201d\uff0c\u7b2c\u4e09\u79cd\u662f\u201c\u76f8\u5bf9\u53e6\u4e00\u6761\u53c2\u8003\u8def\u5f84\u7684\u4f4d\u7f6e\u201d\u3002\u6e90\u548c\u76ee\u6807\u90fd\u7a7f\u8fc7\u540c\u4e00\u4e2a\u8282\u70b9\u65f6\uff0c\u6709\u673a\u4f1a\u5b9a\u4f4d\u5230\u540c\u4e00\u4efd\u56fe\u5e8f\u5217\u3002\u6e90\u6709\u800c\u76ee\u6807\u4e0d\u7ecf\u8fc7\u7684\u8282\u70b9\uff0c\u5de5\u5177\u4ecd\u53ef\u80fd\u8fd4\u56de\u9644\u8fd1\u7684\u53c2\u8003\u4f4d\u7f6e\u3002\u7406\u89e3\u54ea\u4e00\u7c7b\u8f6c\u6362\u6b63\u5728\u53d1\u751f\uff0c\u9700\u8981\u4fdd\u7559\u56fe\u4f4d\u7f6e\u548c\u5230\u53c2\u8003\u7684\u8ddd\u79bb\u4e24\u9879\uff0c\u5355\u6284\u6700\u540e\u7684\u76ee\u6807\u6570\u5b57\u5e38\u5e38\u4f1a\u4e22\u5931\u5fc5\u8981\u4fe1\u606f\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u628a\u4e00\u4e2a\u65b9\u5411\u4e0d\u660e\u7684\u6570\u5b57\u843d\u5b9e\u5230\u78b1\u57fa<\/h2>\n

\u5b89\u88c5 ODGI 0.9.3 \u540e\uff0c\u6211\u4eec\u7528\u56fe\u6784\u5efa\u547d\u4ee4\u751f\u6210\u4e8c\u8fdb\u5236\u56fe\uff0c\u518d\u5b9e\u9645\u8fd0\u884c\u8def\u5f84\u5bfc\u51fa\u4ee5\u53ca\u4f4d\u7f6e\u67e5\u8be2\u3002\u6240\u6709\u5355\u78b1\u57fa\u68c0\u67e5\u90fd\u4ece\u96f6\u5f00\u59cb\u8ba1\u6570\u3002\u53c2\u8003\u504f\u79fb\u96f6\u843d\u5728\u4e00\u53f7\u8282\u70b9\u7684\u8d77\u70b9\uff0c\u4e24\u6761\u8def\u5f84\u90fd\u4ece\u8fd9\u91cc\u6b63\u5411\u901a\u8fc7\uff0c\u76ee\u6807\u504f\u79fb\u4e5f\u662f\u96f6\u3001\u8ddd\u79bb\u4e3a\u96f6\u3002\u53c2\u8003\u504f\u79fb\u4e8c\u5341\u4e94\u843d\u5728\u4e09\u53f7\u8282\u70b9\u5185\u7684\u504f\u79fb\u4e09\uff0c\u76ee\u6807\u504f\u79fb\u4e09\u5341\uff0c\u8ddd\u79bb\u4ecd\u4e3a\u96f6\u3002\u6b64\u5904\u76ee\u6807\u6bd4\u6e90\u591a\u51fa\u7684\u4e94\u4e2a\u78b1\u57fa\u90fd\u5728\u4e0a\u6e38\uff0c\u65b9\u5411\u76f8\u540c\uff0c\u624b\u5de5\u68c0\u67e5 FASTA \u76f8\u5e94\u4f4d\u7f6e\u53ef\u4ee5\u5bf9\u4e0a\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n\n
\u8f93\u5165\u8def\u5f84\u4e0e\u504f\u79fb<\/th>\n\u8fd4\u56de\u7684\u76ee\u6807\u504f\u79fb<\/th>\n\u5230\u53c2\u8003\u8ddd\u79bb<\/th>\n\u76f8\u5bf9\u65b9\u5411<\/th>\n\u72ec\u7acb\u6838\u5bf9<\/th>\n<\/tr>\n<\/thead>\n
ref,0<\/td>\nalt,0<\/td>\n0<\/td>\n\u6b63<\/td>\n\u5171\u4eab\u8d77\u70b9<\/td>\n<\/tr>\n
ref,12<\/td>\nalt,25<\/td>\n0<\/td>\n\u53cd<\/td>\n\u6e90 T \u7684\u4e92\u8865 A \u5728 alt \u96f6\u8d77\u70b9 24<\/td>\n<\/tr>\n
ref,19<\/td>\nalt,18<\/td>\n0<\/td>\n\u53cd<\/td>\n\u6e90 C \u7684\u4e92\u8865 G \u5728 alt \u96f6\u8d77\u70b9 17<\/td>\n<\/tr>\n
ref,25<\/td>\nalt,30<\/td>\n0<\/td>\n\u6b63<\/td>\n\u540c\u4e00\u5171\u4eab\u8282\u70b9\u7684\u6b63\u5411\u4f4d\u7f6e<\/td>\n<\/tr>\n
alt,12<\/td>\nref,10<\/td>\n5<\/td>\n\u6b63<\/td>\n\u6e90\u5728\u4ec5 alt \u5305\u542b\u7684\u4e94\u78b1\u57fa\u8282\u70b9\u4e2d<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u53cd\u5411\u7684\u7b2c\u4e00\u884c\u503c\u5f97\u81ea\u5df1\u7b97\u4e00\u904d\u3002\u53c2\u8003\u504f\u79fb\u5341\u4e8c\u4f4d\u4e8e\u4e8c\u53f7\u8282\u70b9\u5185\u90e8\u7684\u504f\u79fb\u4e8c\u3002\u4ece\u76ee\u6807\u5de6\u4fa7\u5f00\u59cb\uff0c\u524d\u9762\u4e00\u53f7\u52a0\u4e0a\u56db\u53f7\u5171\u5341\u4e94\u78b1\u57fa\u3002\u957f\u5ea6\u5341\u4e8c\u7684\u4e8c\u53f7\u8282\u70b9\u5728\u76ee\u6807\u4e0a\u53cd\u5411\u901a\u8fc7\uff0c\u56e0\u6b64\u5bf9\u5e94\u78b1\u57fa\u7684\u96f6\u8d77\u70b9\u4e0b\u6807\u662f\u5341\u4e94\u52a0\u4e0a\u5341\u4e00\u51cf\u4e8c\uff0c\u5f97\u5230\u4e8c\u5341\u56db\u3002\u53c2\u8003 FASTA \u7684\u5341\u4e8c\u4f4d\u662f T\uff0c\u76ee\u6807\u4e8c\u5341\u56db\u4f4d\u662f A\uff0c\u76ee\u6807\u4e8c\u5341\u4e94\u4f4d\u5374\u662f G\u3002\u53e6\u4e00\u4e2a\u53cd\u5411\u6d4b\u8bd5\u4e5f\u590d\u73b0\u4e86\u6070\u597d\u76f8\u5dee\u4e00\u4f4d\u7684\u60c5\u5f62\u3002\u7531\u6b64\u80fd\u786e\u8ba4\uff0c\u5728\u8fd9\u4e2a\u7248\u672c\u3001\u8fd9\u4e2a\u547d\u4ee4\u548c\u8fd9\u4e24\u5904\u53cd\u5411\u8f93\u51fa\u4e0a\uff0c\u76f4\u63a5\u628a\u8f93\u51fa\u6570\u5b57\u4f5c\u4e3a\u5b57\u7b26\u4e32\u96f6\u8d77\u70b9\u4e0b\u6807\uff0c\u4f1a\u53d6\u9519\u78b1\u57fa\u3002\u6240\u6d4b\u7248\u672c\u7684 position \u5b9e\u73b0<\/a><\/p>\n

\"\u8f93\u51fa\u4e86\u5750\u6807\uff0c\u78b1\u57fa\u5bf9\u5f97\u4e0a\u5417\u3002\u56db\u4e2a\u8282\u70b9\u3001\u4e24\u6761\u8def\u5f84\uff0c\u5206\u522b\u68c0\u67e5\u6b63\u5411\u3001\u53cd\u5411\u548c\u72ec\u6709\u8282\u70b9\u3002\u6b63\u5411\u5171\u4eab\uff0cref
\u56db\u4e2a\u8282\u70b9\u3001\u4e24\u6761\u8def\u5f84\uff0c\u5206\u522b\u68c0\u67e5\u6b63\u5411\u3001\u53cd\u5411\u548c\u72ec\u6709\u8282\u70b9\u3002<\/figcaption><\/figure>\n

\u4e0d\u8981\u628a\u8fd9\u4e2a\u89c2\u5bdf\u7b80\u5316\u6210\u5bf9\u5168\u8868\u7edf\u4e00\u51cf\u4e00\u3002\u8fd9\u6837\u5904\u7406\u4f1a\u628a\u539f\u672c\u6b63\u786e\u7684\u6b63\u5411\u8d77\u70b9\u79fb\u5230\u5e8f\u5217\u4e4b\u5916\u3002\u505a\u533a\u95f4\u6216\u5355\u78b1\u57fa\u8f6c\u6362\u65f6\uff0c\u5e94\u5148\u8bf4\u660e\u6570\u5b57\u4ee3\u8868\u78b1\u57fa\u8fd8\u662f\u8fb9\u754c\uff0c\u8f93\u5165\u8f93\u51fa\u5141\u8bb8\u4f55\u79cd\u94fe\u65b9\u5411\u3001\u5750\u6807\u4ece\u54ea\u91cc\u8d77\u7b97\u3002\u96f6\u8d77\u70b9\u534a\u5f00\u533a\u95f4\u7684\u4e24\u7aef\u63cf\u8ff0\u8fb9\u754c\uff0c\u4e00\u4e2a\u53cd\u5411\u533a\u95f4\u7684\u5de6\u53f3\u5173\u7cfb\u4e5f\u4f1a\u53cd\u8f6c\u3002\u5bf9\u771f\u5b9e\u6d41\u7a0b\u5148\u9020\u4e00\u6bb5\u53ef\u8fa8\u8ba4\u7684\u5e8f\u5217\uff0c\u6d4b\u8bd5\u6b63\u5411\u4e24\u7aef\u3001\u53cd\u5411\u4e24\u7aef\u548c\u5185\u90e8\u4f4d\u7f6e\uff0c\u5206\u522b\u4ece\u8f93\u51fa FASTA \u62bd\u53d6\u78b1\u57fa\u4e0e\u539f\u5e8f\u5217\u6216\u53cd\u5411\u4e92\u8865\u6838\u5b9e\u3002\u5347\u7ea7\u7248\u672c\u65f6\u628a\u8fd9\u4e9b\u6d4b\u8bd5\u4e00\u8d77\u91cd\u8dd1\u3002<\/p>\n

odgi build -g toy.gfa -o graph.og -t 1\r\nodgi paths -i graph.og -f > paths.fa\r\nodgi position -i graph.og -p ref,12,+ -v -t 1\r\nodgi position -i graph.og -p ref,12,+ -r alt -t 1\r\nodgi position -i graph.og -p alt,12,+ -r ref -t 1\r\n<\/code><\/pre>\n
\u53e6\u4e00\u79cd\u8f85\u52a9\u68c0\u67e5\u662f\u56de\u6295\u3002\u628a\u53cd\u5411\u793a\u4f8b\u8fd4\u56de\u7684\u76ee\u6807\u4f4d\u7f6e\u91cd\u65b0\u4f5c\u4e3a\u8f93\u5165\uff0c\u4ecd\u53ef\u80fd\u5f97\u5230\u4e00\u5f00\u59cb\u7ed9\u5b9a\u7684\u6e90\u4f4d\u7f6e\u3002\u8fd9\u8bf4\u660e\u4e24\u4e2a\u65b9\u5411\u7684\u8f6c\u6362\u89c4\u5219\u53ef\u4ee5\u4e92\u76f8\u914d\u5957\uff0c\u5374\u4e0d\u80fd\u5355\u72ec\u8bc1\u660e\u628a\u4e2d\u95f4\u90a3\u4e2a\u6570\u5b57\u5f53\u4f5c FASTA \u4e0b\u6807\u65f6\u53d6\u51fa\u7684\u662f\u6b63\u786e\u78b1\u57fa\u3002\u8bb0\u5f55\u201c\u80fd\u56de\u5230\u539f\u70b9\u201d\u548c\u201c\u4e2d\u95f4\u5e8f\u5217\u6838\u5bf9\u4e00\u81f4\u201d\u4e24\u4e2a\u72ec\u7acb\u7ed3\u679c\uff0c\u4f1a\u6bd4\u53ea\u8bb0\u4e00\u6b21\u5f80\u8fd4\u6210\u529f\u66f4\u6709\u5224\u65ad\u529b\u3002\u524d\u8005\u53ef\u53d1\u73b0\u8d70\u5230\u4e86\u53e6\u4e00\u6761\u91cd\u590d\u8def\u5f84\uff0c\u540e\u8005\u53ef\u66b4\u9732\u7aef\u70b9\u4e0e\u78b1\u57fa\u4e0b\u6807\u4e4b\u95f4\u7684\u504f\u5dee\u3002<\/p>\n
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