{"id":71346,"date":"2026-11-15T00:32:36","date_gmt":"2026-11-14T16:32:36","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71346"},"modified":"2026-11-15T00:32:36","modified_gmt":"2026-11-14T16:32:36","slug":"ragtag-reference-scaffolding-gap-n-coordinate-shift","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/ragtag-reference-scaffolding-gap-n-coordinate-shift\/","title":{"rendered":"RagTag \u5b9e\u8dd1\uff5c\u540c\u4e00\u7ec4 contig \u6302\u5230\u540c\u4e00\u53c2\u8003\uff0c\u4e3a\u4ec0\u4e48 scaffold \u4f1a\u51ed\u7a7a\u957f\u51fa 7400 bp\uff1f"},"content":{"rendered":"
\n

\u7528\u8fd1\u7f18\u57fa\u56e0\u7ec4\u5c06\u788e\u7247\u5316\u7ec4\u88c5\u6302\u8f7d\u5230\u67d3\u8272\u4f53\u540e\uff0c\u7ed3\u679c\u8868\u91cc\u591a\u51fa\u51e0\u5343\u4e2a\u78b1\u57fa\uff0c\u5bb9\u6613\u88ab\u5199\u6210\u201c\u6062\u590d\u4e86\u7f3a\u5931\u5e8f\u5217\u201d\u3002\u5224\u65ad\u662f\u5426\u771f\u7684\u627e\u56de\u5e8f\u5217\uff0c\u53ef\u4ee5\u505a\u4e00\u4e2a\u5f88\u76f4\u89c2\u7684\u68c0\u67e5\uff0c\u628a FASTA \u62c6\u6210\u5df2\u77e5\u78b1\u57fa\u548c\u672a\u77e5\u78b1\u57fa\u4e24\u90e8\u5206\uff0c\u518d\u95ee\u591a\u51fa\u6765\u7684\u5168\u662f\u4ec0\u4e48\u3002\u6211\u4eec\u5728\u53c2\u8003\u4e0a\u4e8b\u5148\u7559\u51fa\u4e03\u5343\u4e94\u767e\u78b1\u57fa\u7684\u95f4\u8ddd\uff0c\u7528 RagTag \u6302\u8f7d\u540c\u6837\u7684\u4e24\u4e2a\u7247\u6bb5\uff0c\u4e8c\u8005\u7684\u6392\u5217\u65b9\u5411\u5b8c\u5168\u4e00\u81f4\uff0c\u53ea\u6539\u4e00\u4e2a\u53c2\u6570\u5c31\u4f7f scaffold \u589e\u957f\u4e03\u5343\u56db\u767e\u3002\u591a\u51fa\u6765\u7684\u4f4d\u7f6e\u6bcf\u4e00\u4e2a\u90fd\u662f N\u3002RagTag scaffold \u5b98\u65b9\u8bf4\u660e<\/a><\/p>\n

\u5728\u53c2\u8003\u4e0a\u6316\u4e00\u4e2a\u77e5\u9053\u957f\u5ea6\u7684\u7f3a\u53e3<\/h2>\n

\u751f\u6210\u4e00\u6761\u957f\u5341\u56db\u4e07\u78b1\u57fa\u7684\u53c2\u8003\u3002\u622a\u53d6\u96f6\u57fa\u533a\u95f4\u4e94\u5343\u5230\u4e94\u4e07\u4e94\u5343\u4f5c\u4e3a\u5de6\u7247\u6bb5\uff0c\u957f\u4e94\u4e07\u3002\u53e6\u53d6\u516d\u4e07\u4e8c\u5343\u4e94\u767e\u5230\u5341\u4e8c\u4e07\u4e94\u5343\u4f5c\u4e3a\u53f3\u7247\u6bb5\uff0c\u957f\u516d\u4e07\u4e8c\u5343\u4e94\u767e\u3002\u4e24\u4e2a\u7247\u6bb5\u76f8\u8ddd\u4e03\u5343\u4e94\u767e\uff0c\u4f4d\u4e8e\u4e24\u7aef\u4e4b\u5916\u7684\u53c2\u8003\u5e8f\u5217\u4e5f\u6ca1\u6709\u52a0\u5165\u67e5\u8be2\u3002\u6545\u610f\u5c06\u53f3\u7247\u6bb5\u5199\u6210\u53cd\u5411\u4e92\u8865\uff0c\u4ee5\u4fbf\u68c0\u9a8c\u6302\u8f7d\u8fc7\u7a0b\u6709\u6ca1\u6709\u8bc6\u522b\u65b9\u5411\u3002\u6700\u540e\u518d\u7ed9\u67e5\u8be2\u52a0\u5165\u4e00\u4e2a\u5168\u65b0\u751f\u6210\u7684\u4e8c\u4e07\u516b\u5343\u78b1\u57fa\u7247\u6bb5\uff0c\u5b83\u5728\u53c2\u8003\u4e0a\u627e\u4e0d\u5230\u5bf9\u5e94\u4f4d\u7f6e\uff0c\u7528\u6765\u89c2\u5bdf\u201c\u672a\u6302\u8f7d\u201d\u5230\u5e95\u662f\u88ab\u4e22\u5f03\u3001\u9644\u5728\u672b\u5c3e\uff0c\u8fd8\u662f\u53e6\u884c\u4fdd\u7559\u3002<\/p>\n

\u4e24\u8f6e\u90fd\u8fd0\u884c RagTag 2.1.1\uff0c\u5e95\u5c42\u4f7f\u7528\u540c\u4e00\u7248 minimap2 \u548c\u76f8\u540c\u67e5\u8be2\u3002\u4f7f\u7528\u7ed9\u672a\u653e\u7f6e\u7247\u6bb5\u6dfb\u52a0\u540e\u7f00\u7684\u9009\u9879\uff0c\u4fdd\u8bc1\u8f93\u5165\u90e8\u4ef6\u540d\u4e0e\u65b0\u6302\u8f7d\u540d\u6613\u4e8e\u533a\u5206\u3002\u7b2c\u4e00\u8f6e\u91c7\u7528\u9ed8\u8ba4\u95f4\u9694\uff0c\u7b2c\u4e8c\u8f6e\u8981\u6c42\u8f6f\u4ef6\u6839\u636e\u53c2\u8003\u6bd4\u5bf9\u63a8\u65ad\u95f4\u8ddd\u3002\u76ee\u6807\u662f\u7531\u67e5\u8be2\u672c\u8eab\u7684\u78b1\u57fa\u7ec4\u6210\u4e00\u4efd\u6302\u8f7d\u7ed3\u679c\uff0c\u56e0\u6b64\u53c2\u8003\u7684\u5df2\u77e5\u5e8f\u5217\u53ea\u63d0\u4f9b\u6392\u5e8f\u3001\u65b9\u5411\u548c\u95f4\u8ddd\u7684\u4f9d\u636e\u3002\u82e5\u6709\u4eba\u5e0c\u671b\u628a\u53c2\u8003\u78b1\u57fa\u4f5c\u4e3a\u989d\u5916\u4fe1\u606f\u586b\u5165\u7f3a\u53e3\uff0c\u90a3\u5df2\u7ecf\u662f\u53e6\u4e00\u9879\u9700\u660e\u786e\u8bb0\u5f55\u6765\u6e90\u7684\u64cd\u4f5c\uff0c\u4e0d\u80fd\u4ece\u201c\u53c2\u8003\u6307\u5bfc\u6302\u8f7d\u5b8c\u6210\u201d\u51e0\u4e2a\u5b57\u63a8\u65ad\u53d1\u751f\u4e86\u8fd9\u4e00\u6b65\u3002RagTag \u9879\u76ee\u4e0e\u5de5\u5177\u8303\u56f4<\/a><\/p>\n

AGP \u7684\u5e8f\u5217\u884c\u548c\u95f4\u9694\u884c\u5404\u8bb2\u4e00\u4ef6\u4e8b<\/h2>\n

\u9ed8\u8ba4\u8fd0\u884c\u628a\u5de6\u7247\u6bb5\u653e\u5728\u9996\u4f4d\uff0c\u65b9\u5411\u4e3a\u6b63\uff0c\u53f3\u7247\u6bb5\u653e\u5728\u7b2c\u4e8c\u4e2a\u5e8f\u5217\u4f4d\u7f6e\uff0c\u65b9\u5411\u4e3a\u8d1f\u3002\u7531\u4e8e\u8f93\u5165\u65f6\u53f3\u7aef\u4eba\u4e3a\u53cd\u8f6c\uff0c\u6700\u7ec8 FASTA \u7684\u53f3\u4fa7\u6b63\u597d\u9010\u5b57\u7b49\u4e8e\u539f\u53c2\u8003\u5bf9\u5e94\u533a\u95f4\u3002\u4e24\u4e2a\u90e8\u4ef6\u672c\u8eab\u52a0\u8d77\u6765\u662f\u5341\u4e00\u4e07\u4e8c\u5343\u4e94\u767e\u4e2a\u5df2\u77e5\u78b1\u57fa\u3002\u9ed8\u8ba4\u5728\u5b83\u4eec\u4e4b\u95f4\u63d2\u5165\u4e00\u767e\u4e2a N\uff0c\u603b\u957f\u5341\u4e00\u4e07\u4e8c\u5343\u516d\u767e\u3002AGP \u4e2d\u8868\u793a\u8fd9\u6bb5\u95f4\u9694\u7684\u7c7b\u578b\u662f U\uff0c\u8868\u793a\u957f\u5ea6\u672a\u77e5\uff0c\u6807\u51c6\u5360\u4f4d\u503c\u4e3a\u4e00\u767e\u3002\u53ea\u770b FASTA\uff0c\u65e0\u6cd5\u77e5\u9053\u8fd9\u91cc\u7684\u4e00\u767e\u662f\u5b9e\u9a8c\u6d4b\u91cf\u503c\u8fd8\u662f\u7ea6\u5b9a\u503c\uff0c\u67e5\u770b AGP \u80fd\u628a\u8fd9\u4e24\u7c7b\u6765\u6e90\u533a\u5206\u5f00\u3002<\/p>\n

\u7b2c\u4e8c\u8f6e\u7684\u4e24\u6761\u5e8f\u5217\u884c\u4ecd\u4f7f\u7528\u76f8\u540c\u90e8\u4ef6\u3001\u76f8\u540c\u65b9\u5411\u548c\u76f8\u540c\u90e8\u4ef6\u5750\u6807\u3002\u95f4\u9694\u6539\u6210\u4e03\u5343\u4e94\u767e\u4e2a N\uff0c\u95f4\u9694\u7c7b\u578b\u53d8\u6210 N\uff0c\u6302\u8f7d\u603b\u957f\u53d8\u6210\u5341\u4e8c\u4e07\u3002\u8fd9\u4e00\u6539\u53d8\u4f7f\u53f3\u7247\u6bb5\u5728\u65b0\u5750\u6807\u4e2d\u7684\u8d77\u70b9\u4ece\u4e00\u57fa\u7684\u4e94\u4e07\u96f6\u4e00\u767e\u96f6\u4e00\u79fb\u52a8\u5230\u4e94\u4e07\u4e03\u5343\u4e94\u767e\u96f6\u4e00\uff0c\u5dee\u503c\u6b63\u597d\u4e03\u5343\u56db\u767e\u3002\u6362\u53e5\u8bdd\u8bf4\uff0c\u540c\u4e00\u6761\u53f3\u4fa7\u57fa\u56e0\u5728\u8fd9\u4e24\u7248 scaffold \u4e0a\u53ef\u4ee5\u6709\u4e24\u4e2a\u4e0d\u540c\u5750\u6807\uff0c\u5373\u4f7f\u5b83\u5468\u56f4\u7684\u5b9e\u9645\u78b1\u57fa\u9010\u5b57\u76f8\u540c\u3002\u6bd4\u8f83\u4e24\u6b21\u6ce8\u91ca\u65f6\uff0c\u5e94\u8be5\u5148\u901a\u8fc7\u90e8\u4ef6\u6620\u5c04\u5bf9\u9f50\u5750\u6807\uff0c\u518d\u53bb\u6000\u7591\u57fa\u56e0\u662f\u5426\u53d1\u751f\u4e86\u7ed3\u6784\u6539\u53d8\u3002NCBI \u5bf9 AGP \u95f4\u9694\u884c\u7684\u5b9a\u4e49<\/a><\/p>\n

\n\n\n\n\n\n\n
\u8fd0\u884c\u65b9\u5f0f<\/th>\n\u8f93\u5165\u90e8\u4ef6\u8d21\u732e<\/th>\n\u95f4\u9694\u672a\u77e5\u78b1\u57fa<\/th>\n\u6302\u8f7d\u5168\u957f<\/th>\n\u53f3\u90e8\u4ef6\u8d77\u70b9\uff0c\u4e00\u57fa<\/th>\n<\/tr>\n<\/thead>\n
\u9ed8\u8ba4<\/td>\n112500 bp<\/td>\n100 \u4e2a N<\/td>\n112600 bp<\/td>\n50101<\/td>\n<\/tr>\n
\u6839\u636e\u53c2\u8003\u63a8\u65ad\u95f4\u9694<\/td>\n112500 bp<\/td>\n7500 \u4e2a N<\/td>\n120000 bp<\/td>\n57501<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u591a\u51fa\u7684
\u7528\u540c\u4e00\u53c2\u8003\u6302\u8f7d\u540c\u4e00\u6279\u90e8\u4ef6\uff0c\u56fa\u5b9a\u5360\u4f4d\u4e0e\u63a8\u65ad\u95f4\u9694\u751f\u6210\u4e0d\u540c\u5750\u6807\u3002<\/figcaption><\/figure>\n

\u8fd8\u53ef\u4ee5\u7528\u4e00\u4e2a\u4e0d\u5728\u7f3a\u53e3\u9644\u8fd1\u7684\u4f4d\u70b9\u505a\u5750\u6807\u9a8c\u7b97\u3002\u9009\u53f3\u4fa7\u8f93\u5165\u7247\u6bb5\u5012\u6570\u7b2c\u4e00\u4e2a\u78b1\u57fa\uff0c\u5b83\u5728\u53cd\u5411\u4e92\u8865\u4e4b\u540e\u4f1a\u6210\u4e3a\u53f3\u90e8\u4ef6\u7684\u7b2c\u4e00\u4e2a\u78b1\u57fa\uff0c\u6240\u4ee5\u5e94\u5206\u522b\u843d\u5728\u4e24\u4efd\u6302\u8f7d\u7684\u4e24\u4e2a\u8d77\u70b9\u3002\u518d\u9009\u8f93\u5165\u7684\u7b2c\u4e00\u4e2a\u78b1\u57fa\uff0c\u5b83\u5e94\u843d\u5230\u5bf9\u5e94\u90e8\u4ef6\u7684\u672b\u7aef\u3002\u4e24\u7aef\u90fd\u7ecf\u8fc7\u8fd9\u4e2a\u6d4b\u8bd5\uff0c\u80fd\u540c\u65f6\u68c0\u51fa\u5750\u6807\u8d77\u70b9\u5c11\u4e00\u4f4d\u53ca\u9057\u6f0f\u94fe\u5411\u7ffb\u8f6c\u4e24\u79cd\u5e38\u89c1\u9519\u8bef\u3002\u5bf9\u8d1f\u94fe\u7684\u57fa\u56e0\u3001\u5f15\u7269\u548c\u63a2\u9488\u91cd\u65b0\u5b9a\u4f4d\u65f6\uff0c\u53ef\u4ee5\u5148\u7528\u8fd9\u4e2a\u7b80\u5355\u6848\u4f8b\u6821\u51c6\u8f6c\u6362\u811a\u672c\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u4ece\u8f93\u51fa\u6587\u4ef6\u76f4\u63a5\u9a8c\u8bc1\u6bcf\u4e2a\u5b57\u6bb5<\/h2>\n
ragtag.py scaffold -t 2 -u -o fixed_gap ref.fa query.fa\r\nragtag.py scaffold -t 2 -u -r -o inferred_gap ref.fa query.fa\r\nawk -F '\\t' '$5=="U" || $5=="N"{print $1,$2,$3,$5,$6}' inferred_gap\/ragtag.scaffold.agp\r\nsamtools faidx inferred_gap\/ragtag.scaffold.fasta\r\n<\/code><\/pre>\n
\u5148\u7528 AGP \u7684\u6302\u8f7d\u7aef\u70b9\u53cd\u7b97\u6bcf\u6bb5\u6240\u5360\u957f\u5ea6\uff0c\u4e00\u57fa\u95ed\u533a\u95f4\u9700\u8981\u672b\u4f4d\u51cf\u8d77\u70b9\u518d\u52a0\u4e00\u3002\u518d\u5728 FASTA \u4e2d\u5b9e\u9645\u7edf\u8ba1 N \u6570\u3002\u6700\u540e\u53d6\u5de6\u53f3\u4e24\u6bb5\u5177\u4f53\u5e8f\u5217\uff0c\u7b2c\u4e00\u6bb5\u6309\u539f\u5411\u3001\u7b2c\u4e8c\u6bb5\u6309\u53cd\u5411\u4e92\u8865\u4e0e\u8f93\u5165\u6bd4\u5bf9\u3002\u56db\u4e2a\u6570\u5b57\u5e94\u8be5\u4e00\u81f4\uff0c\u5373\u4e24\u4e2a\u8f93\u5165\u90e8\u4ef6\u957f\u5ea6\u3001\u95f4\u9694\u957f\u5ea6\u4ee5\u53ca\u4e09\u8005\u4e4b\u548c\u3002\u66f4\u5b8c\u6574\u7684\u590d\u67e5\u8fd8\u5305\u62ec\u672a\u6302\u8f7d\u6761\u76ee\u3002\u6211\u4eec\u5728\u4e24\u8f6e\u7ed3\u679c\u4e2d\u90fd\u627e\u5230\u4e86\u957f\u5ea6\u4ecd\u4e3a\u4e8c\u4e07\u516b\u5343\u3001\u5e8f\u5217\u4e0e\u8f93\u5165\u5b8c\u5168\u4e00\u6837\u7684\u72ec\u7acb\u6761\u76ee\u3002\u5b83\u6ca1\u6709\u88ab\u786c\u63a5\u5230\u53c2\u8003\u67d3\u8272\u4f53\u672b\u7aef\uff0c\u4e5f\u6ca1\u6709\u4ec5\u56e0\u4e3a\u7f3a\u4e4f\u53c2\u8003\u8bc1\u636e\u5c31\u4ece\u4ea4\u4ed8\u7269\u4e2d\u6d88\u5931\u3002<\/p>\n
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