{"id":71605,"date":"2026-11-15T01:28:09","date_gmt":"2026-11-14T17:28:09","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71605"},"modified":"2026-11-15T01:28:09","modified_gmt":"2026-11-14T17:28:09","slug":"liftoff-extra-gene-copies-complete-exon-mapping","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/liftoff-extra-gene-copies-complete-exon-mapping\/","title":{"rendered":"Liftoff \u5b9e\u8dd1\uff5c\u672a\u6620\u5c04\u57fa\u56e0\u6570\u4e3a\u96f6\uff0c\u4e3a\u4ec0\u4e48\u4e00\u4e2a\u771f\u5b9e\u5b58\u5728\u7684\u989d\u5916\u62f7\u8d1d\u4ecd\u7136\u6ca1\u6709\u6ce8\u91ca\uff1f"},"content":{"rendered":"
\n

\u628a\u65e7\u53c2\u8003\u7684\u57fa\u56e0\u6ce8\u91ca\u8fc1\u79fb\u5230\u65b0\u7ec4\u88c5\uff0c\u7ed3\u679c\u663e\u793a\u6e90\u57fa\u56e0\u5168\u90e8\u6620\u5c04\u6210\u529f\u3001\u5916\u663e\u5b50\u8986\u76d6\u7387\u767e\u5206\u4e4b\u767e\u3002\u6b64\u65f6\u63d0\u4ea4\u65b0\u7ec4\u88c5\u7684\u5168\u5957\u57fa\u56e0\u6570\uff0c\u4f1a\u4e0d\u4f1a\u5c11\u62a5\uff1f\u6211\u4eec\u7528\u4e00\u4e2a\u4e24\u5916\u663e\u5b50\u7684\u57fa\u56e0\u6784\u9020\u4e09\u7ec4\u5bf9\u7167\uff0c\u8ba9\u540c\u4e00\u6bb5\u57fa\u56e0\u5e8f\u5217\u5728\u76ee\u6807\u53c2\u8003\u91cc\u51fa\u73b0\u4e00\u6b21\u6216\u4e24\u6b21\uff0c\u518d\u72ec\u7acb\u6539\u53d8\u662f\u5426\u641c\u7d22\u989d\u5916\u62f7\u8d1d\u3002\u4e09\u6b21\u8fd0\u884c\u7684\u672a\u6620\u5c04\u540d\u5355\u5168\u90e8\u4e3a\u7a7a\uff0c\u8f93\u51fa\u91cc\u5374\u5206\u522b\u53ea\u6709\u4e00\u4e2a\u3001\u4e00\u4e2a\u548c\u4e24\u4e2a\u57fa\u56e0\u3002\u539f\u56e0\u53ef\u4ee5\u5728 GFF \u7b2c\u4e5d\u5217\u548c\u5916\u663e\u5b50\u7684\u7236\u5b50\u5173\u7cfb\u4e2d\u8ffd\u5230\u3002Liftoff \u5b98\u65b9\u9879\u76ee<\/a><\/p>\n

\u4e24\u79cd\u5b8c\u6574\u5ea6\u5bf9\u5e94\u4e24\u5f20\u4e0d\u540c\u7684\u6e05\u5355<\/h2>\n

\u5e38\u89c4\u6ce8\u91ca\u8fc1\u79fb\u4ece\u6765\u6e90\u53c2\u8003\u5df2\u6709\u7684\u57fa\u56e0\u6a21\u578b\u51fa\u53d1\uff0c\u5c1d\u8bd5\u5728\u76ee\u6807\u7ec4\u88c5\u4e2d\u4e3a\u5b83\u4eec\u627e\u5230\u5bf9\u5e94\u4f4d\u7f6e\uff0c\u5e76\u5c3d\u91cf\u4fdd\u7559\u5916\u663e\u5b50\u548c\u8f6c\u5f55\u672c\u7ed3\u6784\u3002\u672a\u6620\u5c04\u57fa\u56e0\u540d\u5355\u5173\u6ce8\u7684\u662f\u6e90\u6e05\u5355\u4e2d\u6709\u591a\u5c11\u57fa\u56e0\u6ca1\u6709\u6210\u529f\u627e\u5230\u5bf9\u5e94\u3002\u82e5\u6765\u6e90\u6e05\u5355\u53ea\u6709\u4e00\u4e2a\u57fa\u56e0\uff0c\u5b83\u5728\u76ee\u6807\u4e2d\u53ea\u8981\u6709\u4e00\u4e2a\u5408\u683c\u4f4d\u7f6e\uff0c\u672a\u6620\u5c04\u540d\u5355\u5c31\u53ef\u4ee5\u4e3a\u7a7a\u3002\u76ee\u6807\u91cc\u53e6\u6709\u7b2c\u4e8c\u4efd\u51e0\u4e4e\u76f8\u540c\u7684\u5b8c\u6574\u5e8f\u5217\uff0c\u662f\u5426\u4f1a\u518d\u8f93\u51fa\u4e00\u4efd\u6ce8\u91ca\uff0c\u53d6\u51b3\u4e8e\u4efb\u52a1\u662f\u5426\u641c\u7d22\u989d\u5916\u62f7\u8d1d\uff0c\u4ee5\u53ca\u8bc1\u636e\u662f\u5426\u6ee1\u8db3\u76f8\u5e94\u6761\u4ef6\u3002Liftoff \u65b9\u6cd5\u8bba\u6587<\/a><\/p>\n

\u56e0\u6b64\u8981\u5728\u5f00\u59cb\u65f6\u5199\u6e05\u7814\u7a76\u76ee\u6807\u3002\u7ed9\u8fd1\u7f18\u7ec4\u88c5\u63d0\u4f9b\u4e00\u4efd\u80fd\u548c\u53c2\u8003\u9010\u57fa\u56e0\u5bf9\u7167\u7684\u521d\u7a3f\uff0c\u548c\u5bfb\u627e\u67d0\u4e2a\u5bb6\u65cf\u5728\u65b0\u54c1\u7cfb\u4e2d\u662f\u5426\u6269\u5f20\uff0c\u9700\u8981\u7684\u6761\u4ef6\u4e0d\u540c\u3002\u524d\u8005\u91cd\u70b9\u770b\u6bcf\u4e2a\u539f\u57fa\u56e0\u662f\u5426\u843d\u5230\u6b63\u786e\u7684\u4f4d\u7f6e\u3001\u526a\u63a5\u7ed3\u6784\u662f\u5426\u4fdd\u7559\u3002\u540e\u8005\u8fd8\u8981\u5bfb\u627e\u6ca1\u88ab\u4e3b\u6620\u5c04\u5360\u7528\u7684\u5019\u9009\u4f4d\u7f6e\uff0c\u5e76\u786e\u8ba4\u8fd9\u4e9b\u989d\u5916\u4f4d\u7f6e\u786e\u5b9e\u5c5e\u4e8e\u4e0d\u91cd\u590d\u7684\u76ee\u6807\u533a\u6bb5\u3002\u5355\u4e00\u7684\u201c\u767e\u5206\u4e4b\u591a\u5c11\u57fa\u56e0\u6620\u5c04\u6210\u529f\u201d\u65e0\u6cd5\u4ee3\u66ff\u76ee\u6807\u7ec4\u88c5\u7684\u57fa\u56e0\u5bb6\u65cf\u62f7\u8d1d\u6570\u7edf\u8ba1\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u540c\u4e00\u76ee\u6807\u6587\u4ef6\uff0c\u5207\u6362\u989d\u5916\u62f7\u8d1d\u641c\u7d22<\/h2>\n

\u6211\u4eec\u751f\u6210\u4e00\u4e2a\u8de8\u5ea6\u4e09\u5343\u4e94\u767e\u78b1\u57fa\u7684\u4eba\u5de5\u57fa\u56e0\u3002\u5de6\u53f3\u5916\u663e\u5b50\u5404\u4e03\u767e\u4e94\u5341\u78b1\u57fa\uff0c\u4e2d\u95f4\u76f8\u9694\u4e24\u5343\u78b1\u57fa\uff0c\u6765\u6e90 GFF \u660e\u786e\u5199\u51fa\u4e00\u4e2a\u57fa\u56e0\u3001\u4e00\u4e2a\u8f6c\u5f55\u672c\u548c\u4e24\u4e2a\u5916\u663e\u5b50\u3002\u7b2c\u4e00\u4efd\u76ee\u6807\u53ea\u6709\u548c\u6e90\u4e00\u81f4\u7684\u67d3\u8272\u4f53\u3002\u7b2c\u4e8c\u4efd\u9664\u8fd9\u6761\u67d3\u8272\u4f53\u5916\uff0c\u8fd8\u5305\u542b\u53e6\u4e00\u6761\u547d\u540d\u4e3a extra \u7684\u5e8f\u5217\uff0c\u91cc\u9762\u653e\u5165\u76f8\u540c\u7684\u6574\u6bb5\u57fa\u56e0\uff0c\u4e24\u4fa7\u5219\u662f\u72ec\u7acb\u751f\u6210\u7684\u968f\u673a\u4fa7\u7ffc\u3002\u4f7f\u7528 Liftoff Python \u5305 1.6.3.2 \u548c minimap2 2.26\uff0c\u5206\u522b\u8dd1\u5355\u62f7\u8d1d\u76ee\u6807\u52a0\u989d\u5916\u641c\u7d22\u3001\u53cc\u62f7\u8d1d\u76ee\u6807\u9ed8\u8ba4\u641c\u7d22\u3001\u53cc\u62f7\u8d1d\u76ee\u6807\u52a0\u989d\u5916\u641c\u7d22\u3002<\/p>\n

\n\n\n\n\n\n\n\n
\u76ee\u6807\u4e0e\u8fd0\u884c\u6a21\u5f0f<\/th>\n\u8f93\u51fa\u57fa\u56e0 \/ \u8f6c\u5f55\u672c \/ \u5916\u663e\u5b50<\/th>\n\u672a\u6620\u5c04\u6e90\u57fa\u56e0<\/th>\n\u7b2c\u4e8c\u4e2a\u4f4d\u7f6e<\/th>\n<\/tr>\n<\/thead>\n
\u5355\u62f7\u8d1d\u76ee\u6807\uff0c\u5f00\u542f\u989d\u5916\u641c\u7d22<\/td>\n1 \/ 1 \/ 2<\/td>\n0<\/td>\n\u65e0<\/td>\n<\/tr>\n
\u53cc\u62f7\u8d1d\u76ee\u6807\uff0c\u9ed8\u8ba4<\/td>\n1 \/ 1 \/ 2<\/td>\n0<\/td>\n\u672a\u62a5\u544a<\/td>\n<\/tr>\n
\u53cc\u62f7\u8d1d\u76ee\u6807\uff0c\u5f00\u542f\u989d\u5916\u641c\u7d22<\/td>\n2 \/ 2 \/ 4<\/td>\n0<\/td>\nextra \u7684 5801\u20139300<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u5728\u7b2c\u4e09\u6b21\u7ed3\u679c\u4e2d\uff0c\u539f\u59cb\u57fa\u56e0\u4ecd\u62a5\u544a\u5728 chrR<\/code> \u7684 5001\u20138500\uff0c\u57fa\u56e0\u5c5e\u6027\u4e2d\u7684 extra_copy_number<\/code> \u4e3a\u96f6\u3002\u989d\u5916\u8bb0\u5f55\u4f4d\u4e8e\u53e6\u4e00\u6761\u5e8f\u5217\uff0c\u57fa\u56e0\u540d\u52a0\u4e86\u540e\u7f00\uff0c\u62f7\u8d1d\u5c5e\u6027\u4e3a\u4e00\u3002\u4e24\u4e2a\u8f6c\u5f55\u672c\u5404\u81ea\u6307\u5411\u81ea\u5df1\u7684\u7236\u57fa\u56e0\uff0c\u56db\u6761\u5916\u663e\u5b50\u4e5f\u5206\u522b\u8fde\u5230\u76f8\u5e94\u8f6c\u5f55\u672c\uff0c\u4e3b\u57fa\u56e0\u4e24\u4e2a\u5916\u663e\u5b50\u6ca1\u6709\u88ab\u9519\u8bef\u6302\u5230\u65b0\u57fa\u56e0\u4e0b\u9762\u3002\u4e09\u4e2a\u8ba1\u6570\u90fd\u6309 GFF \u7279\u5f81\u7c7b\u578b\u5206\u522b\u8ba1\u7b97\uff0c\u82e5\u76f4\u63a5\u628a\u516b\u884c\u6ce8\u91ca\u5f53\u6210\u516b\u4e2a\u57fa\u56e0\uff0c\u5c31\u7b97\u6ca1\u6709\u4efb\u4f55\u6280\u672f\u9519\u8bef\u4e5f\u4f1a\u628a\u7ed3\u679c\u653e\u5927\u56db\u500d\u3002<\/p>\n

\"\u6e90\u57fa\u56e0\u5168\u6620\u5c04\uff0c\u4e5f\u4f1a\u6f0f\u62f7\u8d1d\u3002\u540c\u4e00\u4e2a\u4e24\u5916\u663e\u5b50\u6a21\u578b\uff0c\u4e09\u79cd\u6761\u4ef6\u4e0b\u672a\u6620\u5c04\u6570\u90fd\u662f\u96f6\u3002\u5355\u62f7\u8d1d\u76ee\u6807\uff0c\u5f00\u542f\u989d\u5916\u641c\u7d22\u4e5f\u53ea\u6709
\u540c\u4e00\u4e2a\u4e24\u5916\u663e\u5b50\u6a21\u578b\uff0c\u4e09\u79cd\u6761\u4ef6\u4e0b\u672a\u6620\u5c04\u6570\u90fd\u662f\u96f6\u3002<\/figcaption><\/figure>\n

coverage \u7b49\u4e8e\u4e00\uff0c\u8986\u76d6\u7684\u662f\u54ea\u4e00\u6bb5<\/h2>\n

\u4e24\u6761\u57fa\u56e0\u8bb0\u5f55\u90fd\u7ed9\u51fa coverage=1.0<\/code> \u548c sequence_ID=1.0<\/code>\u3002\u4f5c\u8005\u5b9a\u4e49\u8fd9\u4e24\u4e2a\u57fa\u56e0\u6307\u6807\u65f6\u5173\u6ce8\u5916\u663e\u5b50\u533a\u57df\u7684\u6bd4\u5bf9\u8986\u76d6\u53ca\u5e8f\u5217\u4e00\u81f4\u6027\u3002\u5728\u6211\u4eec\u624b\u5de5\u6784\u9020\u7684\u4f8b\u5b50\u91cc\uff0c\u6574\u6bb5\u57fa\u56e0\u8fde\u540c\u5185\u542b\u5b50\u4e5f\u662f\u9010\u5b57\u590d\u5236\u7684\uff0c\u771f\u503c\u65e9\u5df2\u77e5\u9053\u3002\u771f\u5b9e\u9879\u76ee\u4e0d\u80fd\u56e0\u4e3a\u4e24\u5217\u90fd\u662f\u4e00\uff0c\u5c31\u987a\u52bf\u5199\u51fa\u5185\u542b\u5b50\u548c\u57fa\u56e0\u4e24\u4fa7\u8c03\u63a7\u533a\u4e5f\u5b8c\u5168\u76f8\u540c\u3002\u5e94\u5148\u6309\u5916\u663e\u5b50\u5750\u6807\u4ece\u76ee\u6807\u7ec4\u88c5\u53d6\u5e8f\u5217\uff0c\u518d\u72ec\u7acb\u67e5\u770b\u5185\u542b\u5b50\u3001\u4fa7\u7ffc\u4e0e\u6765\u6e90\u533a\u95f4\u662f\u5426\u8fde\u7eed\u5bf9\u5e94\u3002Liftoff \u8f93\u51fa\u5b57\u6bb5\u5b9a\u4e49<\/a><\/p>\n

\u8fd9\u91cc\u7684\u5916\u663e\u5b50\u5750\u6807\u91c7\u7528 GFF \u7684\u4e00\u5f00\u59cb\u8ba1\u6570\u4e14\u5305\u542b\u4e24\u7aef\u7684\u89c4\u5219\u3002\u4f8b\u5982\u989d\u5916\u4f4d\u7f6e\u7684\u7b2c\u4e00\u6bb5\u662f 5801\u20136550\uff0c\u7b2c\u4e8c\u6bb5\u662f 8551\u20139300\uff0c\u5404\u81ea\u90fd\u6070\u597d\u6709\u4e03\u767e\u4e94\u5341\u4e2a\u78b1\u57fa\u3002\u82e5\u8f6c\u6210 BED \u518d\u63d0\u53d6 FASTA\uff0c\u5e94\u5c06\u8d77\u70b9\u51cf\u4e00\uff0c\u7ec8\u70b9\u4fdd\u7559\uff0c\u540c\u65f6\u4fdd\u5b58\u94fe\u65b9\u5411\u548c\u7236\u8f6c\u5f55\u672c\u3002\u4e0d\u8981\u7528\u6574\u6bb5\u57fa\u56e0\u7684\u8de8\u5ea6\u53bb\u4ee3\u66ff\u8868\u8fbe\u4ea7\u7269\u957f\u5ea6\u3002\u4e24\u4e2a\u5916\u663e\u5b50\u4e4b\u548c\u53ea\u6709\u4e00\u5343\u4e94\u767e\u78b1\u57fa\uff0c\u5269\u4f59\u4e24\u5343\u78b1\u57fa\u5728\u672c\u6a21\u578b\u4e2d\u4f4d\u4e8e\u5185\u542b\u5b50\u91cc\u3002<\/p>\n

liftoff target.fa ref.fa -g ref.gff3 -o main.gff -u main.unmapped -dir work_main -p 1\r\nliftoff target.fa ref.fa -g ref.gff3 -o copies.gff -u copies.unmapped \\\r\n  -dir work_copies -p 1 -copies\r\nawk -F '\\t' '$3=="gene"{print $1,$4,$5,$9}' copies.gff\r\n<\/code><\/pre>\n
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