{"id":71344,"date":"2026-11-15T00:32:33","date_gmt":"2026-11-14T16:32:33","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71344"},"modified":"2026-11-15T00:32:33","modified_gmt":"2026-11-14T16:32:33","slug":"yahs-hic-scaffold-reversed-contig-contact-ablation","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/yahs-hic-scaffold-reversed-contig-contact-ablation\/","title":{"rendered":"YaHS \u5b9e\u8dd1\uff5c\u4e09\u6761 contig \u62fc\u6210\u4e00\u6761\uff0c\u600e\u6837\u5224\u65ad\u987a\u5e8f\u6b63\u786e\u3001\u65b9\u5411\u4e5f\u6b63\u786e\uff1f"},"content":{"rendered":"
\n

\u62ff\u5230 Hi-C \u8f85\u52a9\u7ec4\u88c5\u7684\u7ed3\u679c\uff0c\u6709\u4eba\u4f1a\u5bf9\u7167\u53c2\u8003\u4ece\u5de6\u5230\u53f3\u9010\u4e2a\u770b\u7247\u6bb5\u540d\u3002\u9884\u671f\u662f\u7532\u3001\u4e59\u3001\u4e19\uff0c\u7a0b\u5e8f\u5374\u7ed9\u51fa\u4e19\u3001\u4e59\u3001\u7532\uff0c\u662f\u5426\u610f\u5473\u7740\u6574\u6761\u67d3\u8272\u4f53\u62fc\u53cd\u4e86\uff1f\u5982\u679c\u6574\u6761\u53cc\u94fe DNA \u8fde\u540c\u6bcf\u4e2a\u7247\u6bb5\u7684\u65b9\u5411\u4e00\u8d77\u7ffb\u8f6c\uff0c\u4e24\u79cd\u5199\u6cd5\u53ef\u4ee5\u8868\u793a\u540c\u4e00\u4e2a\u8fde\u63a5\u3002\u6211\u4eec\u5148\u5728\u4e00\u4e2a\u5df2\u77e5\u987a\u5e8f\u7684\u5c0f\u57fa\u56e0\u7ec4\u4e0a\u7528 YaHS \u505a\u771f\u5b9e\u6302\u8f7d\uff0c\u518d\u4ece\u8f93\u5165\u4e2d\u62ff\u6389\u4e00\u7ec4\u7279\u5b9a\u7684\u63a5\u89e6\uff0c\u770b\u770b\u54ea\u4e2a\u8fde\u63a5\u771f\u7684\u5931\u53bb\u652f\u6301\u3002\u4e24\u6b21\u7684\u7247\u6bb5\u5e8f\u5217\u5206\u6beb\u672a\u52a8\uff0c\u53d8\u5316\u53d1\u751f\u5728\u54ea\u4e2a\u4f4d\u7f6e\u53ef\u4ee5\u76f4\u63a5\u4ece AGP \u91cd\u5efa\u3002YaHS \u4f5c\u8005\u7684\u7b97\u6cd5\u8bf4\u660e<\/a><\/p>\n

\u8ba9\u4e00\u4e2a\u7247\u6bb5\u5728\u8f93\u5165\u65f6\u5c31\u53cd\u5411<\/h2>\n

\u6a21\u62df\u4e09\u6761\u5404\u4e8c\u5341\u4e07\u78b1\u57fa\u7684\u72ec\u7279\u5e8f\u5217\uff0c\u539f\u59cb\u67d3\u8272\u4f53\u4ece\u5de6\u5230\u53f3\u4f9d\u6b21\u4e3a\u7532\u3001\u4e59\u3001\u4e19\u3002\u5199\u5165\u5f85\u6302\u8f7d\u7684 FASTA \u65f6\uff0c\u7532\u548c\u4e19\u4fdd\u6301\u539f\u65b9\u5411\uff0c\u4e59\u5199\u6210\u53cd\u5411\u4e92\u8865\u3002\u56e0\u6b64\u6309\u8f93\u5165\u6587\u4ef6\u7ed9\u90e8\u4ef6\u6807\u65b9\u5411\uff0c\u671f\u671b\u8fde\u63a5\u662f\u6b63\u7532\u3001\u53cd\u4e59\u3001\u6b63\u4e19\u3002\u5728\u957f\u5206\u5b50\u4e0a\u7684\u4e24\u4e2a\u63a5\u89e6\u70b9\u6309\u968f\u8ddd\u79bb\u8870\u51cf\u7684\u7b80\u5316\u5206\u5e03\u62bd\u6837\uff0c\u968f\u540e\u624d\u6620\u5c04\u56de\u4e09\u4e2a\u8f93\u5165\u7247\u6bb5\u81ea\u5df1\u7684\u5750\u6807\u3002\u7b2c\u4e00\u4e2a\u70b9\u82e5\u843d\u5728\u53cd\u5411\u5199\u51fa\u7684\u4e59\u4e0a\uff0c\u5750\u6807\u4e5f\u8981\u7528\u7247\u6bb5\u957f\u5ea6\u51cf\u4e00\u51cf\u53bb\u539f\u5750\u6807\u3002\u53ea\u6362\u540d\u5b57\u3001\u4e0d\u6362\u5750\u6807\u7684\u6a21\u62df\uff0c\u4f1a\u7ed9\u6302\u8f7d\u7a0b\u5e8f\u5236\u9020\u51fa\u4e00\u4e2a\u9519\u8bef\u7684\u65b9\u5411\u3002<\/p>\n

\u5171\u751f\u6210\u5341\u4e8c\u4e07\u6761\u4eba\u5de5\u63a5\u89e6\u5bf9\uff0c\u7ed9\u4e24\u7aef\u76f8\u540c\u7684\u9ad8\u6bd4\u5bf9\u8d28\u91cf\u3002\u8f93\u5165\u91c7\u7528\u6bcf\u884c\u4e00\u5bf9\u7684\u8def\u5f84\u683c\u5f0f\uff0c\u4fdd\u5b58\u8bfb\u5bf9\u540d\u3001\u4e24\u4e2a\u7247\u6bb5\u540d\u3001\u5404\u81ea\u4f4d\u7f6e\u548c\u4e24\u7aef\u6bd4\u5bf9\u8d28\u91cf\u3002\u6211\u4eec\u5b9e\u9645\u5b89\u88c5\u4e86 YaHS 1.2.2\uff0c\u5e76\u7528\u7d22\u5f15\u597d\u7684\u76f8\u540c\u5e8f\u5217\u8fd0\u884c\u4e24\u6b21\u3002\u7b2c\u4e00\u8f6e\u4fdd\u7559\u5168\u90e8\u63a5\u89e6\uff0c\u7b2c\u4e8c\u8f6e\u53ea\u53bb\u6389\u8fde\u63a5\u7532\u4e0e\u4e59\u7684\u516d\u5343\u4e8c\u767e\u4e00\u5341\u516d\u6761\uff0c\u5269\u5341\u4e00\u4e07\u4e09\u5343\u4e03\u767e\u516b\u5341\u56db\u6761\u3002\u4e59\u4e0e\u4e19\u4e4b\u95f4\u7684\u516d\u5343\u4e09\u767e\u4e00\u5341\u4e8c\u6761\u5168\u90e8\u4fdd\u7559\uff0c\u6bcf\u6761\u7247\u6bb5\u5185\u90e8\u7684\u63a5\u89e6\u4e5f\u539f\u6837\u4fdd\u7559\u3002\u4e3a\u628a\u95ee\u9898\u96c6\u4e2d\u5728\u6302\u8f7d\uff0c\u4e24\u8f6e\u90fd\u5173\u95ed\u7247\u6bb5\u7ea0\u9519\u548c\u540e\u7eed\u6302\u8f7d\u7ea0\u9519\uff0c\u4f7f\u7528\u76f8\u540c\u5206\u8fa8\u7387\u3002YaHS \u8f93\u5165\u4e0e\u53c2\u6570<\/a><\/p>\n

\u4ece AGP \u91cd\u5efa\u8fde\u63a5\uff0c\u4e0d\u9760 FASTA \u6807\u9898\u731c\u65b9\u5411<\/h2>\n

\u7b2c\u4e00\u8f6e\u7ed3\u679c\u662f\u4e00\u6761\u957f\u516d\u5341\u4e07\u96f6\u4e8c\u767e\u78b1\u57fa\u7684 scaffold\u3002\u4f9d\u6b21\u8bfb\u53d6\u4e09\u4e2a\u5e8f\u5217\u90e8\u4ef6\uff0c\u662f\u53cd\u4e19\u3001\u6b63\u4e59\u3001\u53cd\u7532\u3002\u628a\u6574\u4e2a\u7ed3\u679c\u5012\u8fc7\u6765\u8bfb\uff0c\u540c\u65f6\u5bf9\u6bcf\u4e2a\u90e8\u4ef6\u53d6\u53cd\uff0c\u4fbf\u5f97\u5230\u6b63\u7532\u3001\u53cd\u4e59\u3001\u6b63\u4e19\uff0c\u4e0e\u8bbe\u8ba1\u5b8c\u5168\u4e00\u81f4\u3002\u82e5\u53ea\u53cd\u8f6c\u7247\u6bb5\u987a\u5e8f\u800c\u4e0d\u5207\u6362\u5404\u81ea\u7b26\u53f7\uff0c\u5c31\u4f1a\u9519\u5224\u4e59\u76f8\u5bf9\u4e24\u4fa7\u7684\u65b9\u5411\u3002\u5bf9\u4e8e\u6ca1\u6709\u5916\u90e8\u67d3\u8272\u4f53\u65b9\u5411\u6807\u8bb0\u7684\u6302\u8f7d\uff0c\u5148\u770b\u54ea\u4e24\u4e2a\u7aef\u70b9\u76f8\u90bb\uff0c\u518d\u770b\u6574\u6761\u67d3\u8272\u4f53\u8be5\u4ee5\u54ea\u4e00\u7aef\u4f5c\u4e3a\u663e\u793a\u8d77\u70b9\u3002\u540e\u4e00\u9879\u53ef\u4ee5\u968f\u5c55\u793a\u7ea6\u5b9a\u6539\u53d8\uff0c\u524d\u4e00\u9879\u76f4\u63a5\u5f71\u54cd\u8de8\u65ad\u70b9\u57fa\u56e0\u4e0e\u7ed3\u6784\u89e3\u91ca\u3002<\/p>\n

\u4e09\u4e2a\u5e8f\u5217\u90e8\u4ef6\u7684\u957f\u5ea6\u603b\u548c\u59cb\u7ec8\u662f\u516d\u5341\u4e07\u3002\u7b2c\u4e00\u8f6e\u5728\u4e24\u4e2a\u63a5\u5934\u5404\u6dfb\u52a0\u4e00\u767e\u4e2a\u672a\u77e5\u78b1\u57fa\u4f5c\u5360\u4f4d\uff0cAGP \u7528 U \u8868\u793a\u957f\u5ea6\u672a\u786e\u5b9a\u7684\u95f4\u9694\uff0c\u8fde\u63a5\u8bc1\u636e\u5199\u660e\u6765\u81ea\u90bb\u8fd1\u8fde\u63a5\u5b9e\u9a8c\u3002\u56e0\u6b64\u6700\u540e\u6bd4\u771f\u5b9e\u5e8f\u5217\u591a\u4e8c\u767e\uff0c\u5e76\u4e0d\u610f\u5473\u7740\u7a0b\u5e8f\u6d4b\u5230\u4e86\u4e24\u6bb5\u5404\u4e00\u767e\u78b1\u57fa\u7684\u65b0\u5e8f\u5217\u3002\u8981\u7edf\u4e00\u591a\u4e2a\u7248\u672c\u7684\u7ec4\u88c5\u603b\u957f\uff0c\u53ef\u4ee5\u540c\u65f6\u62a5\u544a\u5e8f\u5217\u90e8\u4ef6\u78b1\u57fa\u6570\u3001\u95f4\u9694\u5360\u4f4d\u6570\u4ee5\u53ca\u5305\u542b\u95f4\u9694\u7684\u6302\u8f7d\u957f\u5ea6\u3002\u9047\u5230\u8fde\u7eed\u7684\u672a\u77e5\u78b1\u57fa\u65f6\uff0c\u518d\u67e5\u5b83\u4eec\u662f\u539f\u59cb\u7247\u6bb5\u5185\u90e8\u672c\u6765\u5b58\u5728\u7684\uff0c\u8fd8\u662f\u6b64\u6b21\u6302\u8f7d\u65b0\u6dfb\u7684\u3002NCBI AGP \u683c\u5f0f\u89c4\u8303<\/a><\/p>\n

\n\n\n\n\n\n\n
\u63a5\u89e6\u5bf9\u8f93\u5165<\/th>\n\u7247\u6bb5\u95f4\u7684\u6709\u6548\u8fde\u63a5<\/th>\nscaffold \u6570<\/th>\nAGP \u95f4\u9694<\/th>\n<\/tr>\n<\/thead>\n
\u5168\u90e8 120000 \u6761<\/td>\n\u7532\u4e59 6216\u3001\u4e59\u4e19 6312<\/td>\n1<\/td>\n\u4e24\u4e2a\uff0c\u5404 100 bp<\/td>\n<\/tr>\n
\u53bb\u6389\u5168\u90e8\u7532\u4e59\u63a5\u89e6<\/td>\n\u7532\u4e59 0\u3001\u4e59\u4e19\u4ecd 6312<\/td>\n2<\/td>\n\u4e00\u4e2a\uff0c100 bp<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u5220\u53bb\u4e00\u7ec4\u63a5\u89e6\uff0c\u65ad\u5f00\u54ea\u4e00\u5934\u3002\u4e09\u4e2a
\u4e09\u4e2a 200 kb \u7247\u6bb5\u4e2d\u7684\u4e59\u9884\u5148\u53cd\u5411\uff0c\u6309 AGP \u8ffd\u8e2a\u4e24\u4e2a\u63a5\u5934\u3002<\/figcaption><\/figure>\n

\u8fd8\u6709\u4e00\u4e2a\u4e0d\u4f9d\u8d56\u53c2\u8003\u5e8f\u5217\u7684\u68c0\u67e5\u3002\u4e24\u8f6e\u628a\u6240\u6709\u6807\u4e3a\u5e8f\u5217\u90e8\u4ef6\u7684\u884c\u6309\u539f\u59cb\u7247\u6bb5\u540d\u6c47\u603b\uff0c\u786e\u8ba4\u7532\u3001\u4e59\u3001\u4e19\u5404\u51fa\u73b0\u4e00\u6b21\uff0c\u6bcf\u6bb5\u8d77\u70b9\u4e3a\u4e00\u3001\u7ec8\u70b9\u4e3a\u4e8c\u5341\u4e07\u3002\u518d\u5206\u5f00\u6c47\u603b\u4e0d\u540c\u6302\u8f7d\u7684\u672a\u77e5\u95f4\u9694\u3002\u8fd9\u6837\u82e5\u6709\u4e00\u6bb5\u7a81\u7136\u91cd\u590d\u8ba1\u5165\u4e24\u4e2a\u4f4d\u7f6e\uff0c\u6216\u4e00\u6761\u77ed\u7247\u6bb5\u5728\u5904\u7406\u65f6\u88ab\u6084\u6084\u8fc7\u6ee4\uff0c\u5373\u4f7f\u6700\u7ec8\u6302\u8f7d\u7684\u6761\u6570\u5b8c\u5168\u7b26\u5408\u9884\u671f\uff0c\u4e5f\u80fd\u4ece\u539f\u59cb\u90e8\u4ef6\u6e05\u5355\u4e2d\u67e5\u51fa\u6765\u3002\u6362\u7528\u771f\u5b9e\u57fa\u56e0\u7ec4\u65f6\uff0c\u5148\u628a\u88ab\u957f\u5ea6\u9608\u503c\u6392\u9664\u7684\u7247\u6bb5\u5355\u5217\u51fa\u6765\uff0c\u7528\u540c\u4e00\u6279\u8f93\u5165\u5b9a\u4e49\u5206\u6bcd\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u5224\u65ad\u4e00\u4e2a\u5206\u652f\u8981\u770b\u6307\u5b9a\u4e24\u7aef\u7684\u8bc1\u636e<\/h2>\n
samtools faidx contigs.fa\r\nyahs --no-contig-ec --no-scaffold-ec -r 5000,10000,20000 -o all contigs.fa all.pa5\r\nyahs --no-contig-ec --no-scaffold-ec -r 5000,10000,20000 -o reduced contigs.fa no_AB.pa5\r\nawk -F '\\t' '$5=="W"{print $1,$6,$9}' reduced_scaffolds_final.agp\r\n<\/code><\/pre>\n
\u53bb\u6389\u7532\u4e59\u63a5\u89e6\u540e\uff0c\u7b2c\u4e8c\u8f6e\u8f93\u51fa\u4e00\u6761\u7531\u53cd\u4e19\u3001\u6b63\u4e59\u7ec4\u6210\u7684\u6302\u8f7d\uff0c\u53e6\u6709\u4e00\u6761\u72ec\u7acb\u7684\u6b63\u7532\u3002\u4e59\u4e19\u4e4b\u95f4\u7684\u76f8\u5bf9\u987a\u5e8f\u548c\u65b9\u5411\u4e0e\u7b2c\u4e00\u8f6e\u4e00\u81f4\uff0c\u539f\u6765\u7532\u8fde\u5230\u4e59\u7684\u4f4d\u7f6e\u6d88\u5931\u3002\u4e24\u6761\u6302\u8f7d\u52a0\u8d77\u6765\u4f9d\u65e7\u5305\u542b\u5168\u90e8\u516d\u5341\u4e07\u5df2\u77e5\u78b1\u57fa\uff0c\u53ea\u6709\u5360\u4f4d\u51cf\u5c11\u4e86\u4e00\u767e\u3002\u82e5\u53ea\u770b\u603b\u957f\u51e0\u4e4e\u6ca1\u53d8\uff0c\u5f88\u5bb9\u6613\u9519\u8fc7\u4e00\u6b21\u7ed3\u6784\u53d8\u5316\u3002\u53cd\u8fc7\u6765\uff0c\u82e5\u628a\u4e24\u4efd AGP \u4e2d\u540c\u4e00\u4e2a\u7247\u6bb5\u7684\u6b63\u8d1f\u53f7\u9010\u884c\u6c42\u5dee\uff0c\u53c8\u4f1a\u628a\u5355\u72ec\u5b58\u5728\u7684\u7532\u6362\u65b9\u5411\u4e5f\u7edf\u8ba1\u6210\u4e00\u6b21\u751f\u7269\u5b66\u5012\u4f4d\u3002\u53ef\u4ee5\u5148\u5c06\u6bcf\u4e2a\u63a5\u5934\u5199\u6210\u201c\u54ea\u4e2a\u7247\u6bb5\u7684\u54ea\u4e00\u7aef\u8fde\u63a5\u5230\u54ea\u4e00\u7aef\u201d\uff0c\u518d\u6bd4\u8f83\u4e24\u5957\u63a5\u5934\u96c6\u5408\u3002<\/p>\n
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\u6700\u540e\u4fdd\u5b58 AGP \u548c\u6700\u521d\u7684\u8f93\u5165 FASTA\u3002\u53ea\u4fdd\u7559\u6302\u8f7d\u540e\u7684\u5e8f\u5217\u4f1a\u5931\u53bb\u90e8\u4ef6\u65b9\u5411\u4e0e\u539f\u59cb\u63a5\u5934\uff0c\u540e\u7eed\u6539\u52a8\u4e00\u4e2a\u533a\u6bb5\u65f6\u96be\u4ee5\u5224\u65ad\u5750\u6807\u5c5e\u4e8e\u54ea\u4e2a\u7248\u672c\u3002\u5229\u7528 AGP \u7684\u4e00\u57fa\u95ed\u533a\u95f4\u53ef\u9010\u6bb5\u6821\u9a8c\u957f\u5ea6\uff0c\u518d\u628a\u5019\u9009\u57fa\u56e0\u6620\u5c04\u5230\u65b0\u5750\u6807\uff0c\u5bf9\u9760\u8fd1\u672a\u77e5\u95f4\u9694\u7684\u591a\u5916\u663e\u5b50\u6a21\u578b\u5355\u72ec\u590d\u6838\u3002\u8fd9\u6837\u5373\u4f7f\u4ee5\u540e\u53d6\u6d88\u7532\u4e59\u8fde\u63a5\uff0c\u4e5f\u80fd\u8fc5\u901f\u627e\u5230\u54ea\u4e9b\u6ce8\u91ca\u9700\u8981\u91cd\u65b0\u68c0\u67e5\u3002<\/p>\n
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