{"id":73215,"date":"2026-11-15T15:03:39","date_gmt":"2026-11-15T07:03:39","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=73215"},"modified":"2026-11-15T15:03:39","modified_gmt":"2026-11-15T07:03:39","slug":"bedtools-intersect-coverage-fraction-strand-split-practice","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/bedtools-intersect-coverage-fraction-strand-split-practice\/","title":{"rendered":"BEDTools \u5b9e\u8dd1\u590d\u76d8\uff0c100 \u78b1\u57fa\u7684\u533a\u95f4\u4e3a\u4ec0\u4e48\u4f1a\u7b97\u51fa 110 \u78b1\u57fa\u91cd\u53e0"},"content":{"rendered":"
\n

\u628a\u4e00\u7ec4\u5cf0\u4e0e\u6ce8\u91ca\u6c42\u4ea4\u540e\uff0c\u8f93\u51fa\u884c\u6570\u6bd4\u8f93\u5165\u5cf0\u6570\u66f4\u591a\uff0c\u91cd\u53e0\u957f\u5ea6\u76f8\u52a0\u751a\u81f3\u8d85\u8fc7\u5cf0\u672c\u8eab\u7684\u957f\u5ea6\u3002\u8fd9\u4e9b\u73b0\u8c61\u672a\u5fc5\u610f\u5473\u7740\u8f6f\u4ef6\u51fa\u9519\u3002\u5b83\u4eec\u9996\u5148\u63d0\u793a\u6211\u4eec\uff0c\u6b63\u5728\u7edf\u8ba1\u7684\u53ef\u80fd\u662f\u533a\u95f4\u4e4b\u95f4\u7684\u914d\u5bf9\u5173\u7cfb\uff0c\u800c\u4e0d\u662f\u88ab\u6ce8\u91ca\u8986\u76d6\u7684\u72ec\u7acb\u78b1\u57fa\uff0c\u6216\u8005\u6709\u6ce8\u91ca\u7684\u5cf0\u7684\u6570\u91cf\u3002<\/p>\n

\u672c\u6587\u5b9e\u9645\u5b89\u88c5\u5e76\u8fd0\u884c BEDTools 2.31.1\uff0c\u7528\u81ea\u884c\u6784\u9020\u7684\u56db\u4e2a\u67e5\u8be2\u533a\u95f4\u548c\u516d\u4e2a\u6ce8\u91ca\u533a\u95f4\uff0c\u4f9d\u6b21\u6838\u5bf9\u914d\u5bf9\u3001\u8986\u76d6\u3001\u6bd4\u4f8b\u95e8\u69db\u3001\u94fe\u65b9\u5411\u3001\u76f8\u90bb\u533a\u95f4\u5408\u5e76\u3001\u8f6c\u5f55\u672c\u5206\u5757\u548c\u6392\u5e8f\u68c0\u67e5\u3002\u6bcf\u4e00\u4e2a\u6570\u5b57\u90fd\u6765\u81ea\u672c\u6b21\u8f93\u51fa\uff0c\u8bfb\u8005\u53ef\u4ee5\u7528\u7eb8\u7b14\u590d\u7b97\u3002\u8fd9\u91cc\u6ca1\u6709\u771f\u5b9e\u6d4b\u5e8f\u6570\u636e\uff0c\u4e5f\u6ca1\u6709\u901a\u8fc7\u5c0f\u4f8b\u5b50\u7684\u8017\u65f6\u63a8\u6d4b\u5168\u57fa\u56e0\u7ec4\u6027\u80fd\u3002<\/p>\n

\"100
\u81ea\u5efa\u533a\u95f4\u5b9e\u8dd1 \u00b7 \u914d\u5bf9\u3001\u8986\u76d6\u4e0e\u7b5b\u9009\u7684\u4e0d\u540c\u5206\u6bcd<\/figcaption><\/figure>\n

\u4e00\u3001\u5148\u5199\u6e05\u695a\uff0c\u4e00\u884c\u5230\u5e95\u4ee3\u8868\u4ec0\u4e48<\/h2>\n

\u67e5\u8be2\u6587\u4ef6\u4e2d\u7684\u56db\u4e2a\u533a\u95f4\u5206\u522b\u53eb\u4f5c\u7532\u3001\u4e59\u3001\u4e19\u3001\u4e01\uff0c\u5bf9\u5e94\u811a\u672c\u91cc\u7684 P1 \u5230 P4\u3002\u5b83\u4eec\u4f4d\u4e8e\u540c\u4e00\u6761\u865a\u6784\u67d3\u8272\u4f53\uff0c\u8d77\u6b62\u5750\u6807\u4f9d\u6b21\u662f 100 \u5230 200\u3001200 \u5230 300\u3001500 \u5230 600\u3001700 \u5230 800\uff0c\u957f\u5ea6\u90fd\u4e3a\u4e00\u767e\u3002\u7532\u3001\u4e19\u3001\u4e01\u6807\u8bb0\u6b63\u94fe\uff0c\u4e59\u6807\u8bb0\u8d1f\u94fe\u3002<\/p>\n

\u6ce8\u91ca\u6587\u4ef6\u4e2d\uff0c\u524d\u4e09\u6bb5\u4e3a 90 \u5230 140\u3001130 \u5230 180\u3001180 \u5230 200\uff0c\u90fd\u4e0e\u7532\u76f8\u4ea4\u3002\u968f\u540e\u4e24\u6bb5\u4e3a 200 \u5230 250\u3001250 \u5230 300\uff0c\u90fd\u4e0e\u4e59\u76f8\u4ea4\u3002\u6700\u540e\u4e00\u6bb5\u4e3a 550 \u5230 560\uff0c\u53ea\u4e0e\u4e19\u76f8\u4ea4\u3002\u4e01\u6ca1\u6709\u5bf9\u5e94\u6ce8\u91ca\u3002\u811a\u672c\u4fdd\u7559\u4e86\u6bcf\u4e2a\u6ce8\u91ca\u7684\u540d\u79f0\u548c\u94fe\u65b9\u5411\uff0c\u4e0d\u9700\u8981\u4f9d\u9760\u884c\u53f7\u731c\u6d4b\u8eab\u4efd\u3002<\/p>\n

\u8fd9\u91cc\u4f7f\u7528 BED \u7684\u96f6\u8d77\u70b9\u3001\u53f3\u7aef\u4e0d\u5305\u542b\u7ea6\u5b9a\u3002100 \u5230 200 \u7684\u957f\u5ea6\u662f\u7ec8\u70b9\u51cf\u8d77\u70b9\uff0c\u7b49\u4e8e\u4e00\u767e\u3002200 \u5230 250 \u4e0e\u5b83\u4ec5\u8fb9\u754c\u76f8\u63a5\uff0c\u6ca1\u6709\u5171\u540c\u8986\u76d6\u7684\u78b1\u57fa\u3002\u672c\u6b21\u5355\u72ec\u8fd0\u884c\u8fb9\u754c\u5bf9\u7167\uff0c\u8f6f\u4ef6\u8fd4\u56de\u7684\u91cd\u53e0\u6761\u6570\u786e\u5b9e\u4e3a\u96f6\u3002\u5c06\u4e24\u4e2a\u533a\u95f4\u90fd\u770b\u4f5c\u53cc\u7aef\u5305\u542b\uff0c\u4f1a\u51ed\u7a7a\u521b\u9020\u4e00\u4e2a\u4ea4\u70b9\u3002<\/p>\n

\u5b9e\u9645\u9879\u76ee\u8fd8\u9700\u8981\u68c0\u67e5\u53c2\u8003\u7ec4\u88c5\u7248\u672c\u3001\u67d3\u8272\u4f53\u547d\u540d\u548c\u5750\u6807\u6765\u6e90\u3002\u628a\u67d3\u8272\u4f53\u540d\u79f0\u8865\u4e0a\u524d\u7f00\uff0c\u4e0d\u80fd\u628a\u65e7\u7248\u672c\u5750\u6807\u53d8\u6210\u65b0\u7248\u672c\u5750\u6807\u3002\u5bf9\u7531\u6d4f\u89c8\u5668\u3001\u6ce8\u91ca\u6587\u4ef6\u6216\u624b\u5de5\u8868\u683c\u5bfc\u51fa\u7684\u533a\u57df\uff0c\u6700\u597d\u7559\u4e0b\u539f\u59cb\u683c\u5f0f\u4e0e\u8f6c\u6362\u6b65\u9aa4\uff0c\u518d\u68c0\u67e5\u4e00\u4e24\u4e2a\u5df2\u77e5\u4f4d\u7f6e\u3002\u683c\u5f0f\u6b63\u786e\u4e0e\u751f\u7269\u5b66\u4f4d\u7f6e\u6b63\u786e\u662f\u4e24\u9879\u68c0\u67e5\u3002<\/p>\n

\u4e8c\u3001\u516d\u884c\u8f93\u51fa\uff0c\u4e0d\u4ee3\u8868\u6709\u516d\u4e2a\u5cf0\u5f97\u5230\u6ce8\u91ca<\/h2>\n

\u672c\u6b21\u5e26\u53cc\u65b9\u5b8c\u6574\u8bb0\u5f55\u7684\u6c42\u4ea4\u4ea7\u751f\u516d\u884c\uff0c\u542b\u4e49\u662f\u516d\u5bf9\u67e5\u8be2\u4e0e\u6ce8\u91ca\u5339\u914d\u3002\u7532\u51fa\u73b0\u4e09\u6b21\uff0c\u4e59\u51fa\u73b0\u4e24\u6b21\uff0c\u4e19\u51fa\u73b0\u4e00\u6b21\u3002\u8f93\u51fa\u4e2d\u91cd\u590d\u51fa\u73b0\u7532\uff0c\u662f\u56e0\u4e3a\u5b83\u4e0e\u4e09\u6761\u6ce8\u91ca\u5206\u522b\u5efa\u7acb\u5173\u7cfb\uff0c\u8fd9\u4e09\u884c\u627f\u62c5\u4e86\u4e0d\u540c\u7684\u4fe1\u606f\u3002<\/p>\n

\u5982\u679c\u95ee\u9898\u662f\u201c\u54ea\u4e9b\u67e5\u8be2\u81f3\u5c11\u547d\u4e2d\u8fc7\u4e00\u6761\u6ce8\u91ca\u201d\uff0c\u4f7f\u7528\u53ea\u8f93\u51fa\u547d\u4e2d\u67e5\u8be2\u7684\u6a21\u5f0f\uff0c\u5f97\u5230\u7532\u3001\u4e59\u3001\u4e19\u4e09\u4e2a\u533a\u95f4\u3002\u5982\u679c\u95ee\u9898\u662f\u201c\u6bcf\u4e2a\u67e5\u8be2\u5404\u6709\u51e0\u6761\u547d\u4e2d\u201d\uff0c\u8ba1\u6570\u6a21\u5f0f\u7ed9\u51fa\u4e09\u3001\u4e8c\u3001\u4e00\u3001\u96f6\uff0c\u4ecd\u7136\u4fdd\u7559\u56db\u4e2a\u67e5\u8be2\u3002\u6ca1\u6709\u547d\u4e2d\u7684\u4e01\u4e5f\u5f88\u91cd\u8981\uff0c\u5426\u5219\u8ba1\u7b97\u6ce8\u91ca\u7387\u65f6\uff0c\u5206\u6bcd\u5c31\u5df2\u7ecf\u6084\u6084\u53d8\u6210\u4e86\u7b5b\u9009\u540e\u7684\u96c6\u5408\u3002<\/p>\n

bedtools intersect -a A.bed -b B.bed -wa -wb\r\nbedtools intersect -a A.bed -b B.bed -u\r\nbedtools intersect -a A.bed -b B.bed -c\r\nbedtools intersect -a A.bed -b B.bed -v\r\n<\/code><\/pre>\n
\u8fd9\u51e0\u6761\u547d\u4ee4\u4f7f\u7528\u540c\u6837\u7684\u8f93\u5165\uff0c\u53ea\u6539\u53d8\u8f93\u51fa\u8981\u56de\u7b54\u7684\u95ee\u9898\u3002\u7b2c\u4e00\u6761\u9002\u5408\u4fdd\u5b58\u6ce8\u91ca\u5173\u8054\u8868\uff0c\u7b2c\u4e8c\u6761\u9002\u5408\u7b5b\u51fa\u6709\u547d\u4e2d\u7684\u67e5\u8be2\uff0c\u7b2c\u4e09\u6761\u9002\u5408\u628a\u547d\u4e2d\u6570\u91cf\u4f5c\u4e3a\u67e5\u8be2\u7684\u4e00\u5217\u5c5e\u6027\uff0c\u7b2c\u56db\u6761\u9002\u5408\u8ffd\u8e2a\u672a\u547d\u4e2d\u533a\u57df\u3002\u5c06\u7b2c\u4e00\u6761\u8f93\u51fa\u76f4\u63a5\u6309\u884c\u8ba1\u7b97\u5cf0\u6570\uff0c\u4f1a\u628a\u6ce8\u91ca\u7ed3\u6784\u7684\u590d\u6742\u5ea6\u8bef\u5f53\u6210\u5cf0\u6570\u91cf\u589e\u52a0\u3002<\/p>\n
\u8fd8\u6709\u4e00\u4e2a\u5b9e\u9645\u8dd1\u8fc7\u7684\u7ec6\u8282\u3002\u5c06\u540c\u4e00\u6761\u67e5\u8be2\u5728\u8f93\u5165\u4e2d\u5199\u4e24\u6b21\uff0c\u518d\u4f7f\u7528\u53ea\u4fdd\u7559\u547d\u4e2d\u67e5\u8be2\u7684\u53c2\u6570\uff0c\u8f93\u51fa\u4ecd\u7136\u6709\u4e24\u6761\u76f8\u540c\u8bb0\u5f55\u3002\u8fd9\u4e2a\u53c2\u6570\u907f\u514d\u7684\u662f\u4e00\u6761\u8f93\u5165\u56e0\u591a\u4e2a\u5339\u914d\u800c\u91cd\u590d\u8f93\u51fa\uff0c\u4e0d\u8d1f\u8d23\u628a\u8f93\u5165\u6587\u4ef6\u672c\u6765\u5c31\u5b58\u5728\u7684\u91cd\u590d\u8bb0\u5f55\u5408\u5e76\u3002\u6e05\u7406\u91cd\u590d\u5750\u6807\u3001\u91cd\u590d\u540d\u79f0\u548c\u4fdd\u7559\u4e0d\u540c\u8f6c\u5f55\u672c\uff0c\u5e94\u5728\u660e\u786e\u4e1a\u52a1\u542b\u4e49\u4e4b\u540e\u5206\u522b\u5904\u7406\u3002<\/p>\n
\u4e09\u3001110 \u78b1\u57fa\u6765\u81ea\u91cd\u590d\u7d2f\u8ba1\uff0c\u8986\u76d6\u5bbd\u5ea6\u4ecd\u662f 100<\/h2>\n
\u7532\u4e0e\u524d\u4e09\u6761\u6ce8\u91ca\u7684\u91cd\u53e0\u957f\u5ea6\uff0c\u5b9e\u9645\u8f93\u51fa\u5206\u522b\u4e3a\u56db\u5341\u3001\u4e94\u5341\u3001\u4e8c\u5341\uff0c\u76f8\u52a0\u662f\u4e00\u767e\u4e00\u5341\u3002\u524d\u4e24\u6761\u6ce8\u91ca\u5728 130 \u5230 140 \u7684\u5341\u4e2a\u78b1\u57fa\u8303\u56f4\u5185\u91cd\u5408\uff0c\u56e0\u6b64\u8fd9\u5341\u4e2a\u4f4d\u7f6e\u88ab\u8ba1\u5165\u4e86\u4e24\u6b21\u3002\u4e24\u4e24\u6c42\u4ea4\u7684\u957f\u5ea6\u4e4b\u548c\u9002\u5408\u63cf\u8ff0\u914d\u5bf9\u7d2f\u8ba1\u91cf\uff0c\u4f46\u4e0d\u80fd\u76f4\u63a5\u5f53\u4f5c\u7532\u7684\u975e\u91cd\u590d\u8986\u76d6\u957f\u5ea6\u3002<\/p>\n
\u8fd0\u884c\u8986\u76d6\u7edf\u8ba1\u540e\uff0c\u7532\u7684\u975e\u96f6\u8986\u76d6\u78b1\u57fa\u6570\u4e3a\u4e00\u767e\uff0c\u8986\u76d6\u6bd4\u4f8b\u4e3a\u767e\u5206\u4e4b\u767e\u3002\u8f6f\u4ef6\u540c\u65f6\u62a5\u544a\u4e09\u6761\u6ce8\u91ca\u547d\u4e2d\u3001\u4e00\u767e\u78b1\u57fa\u88ab\u8986\u76d6\u3001\u4e00\u767e\u78b1\u57fa\u67e5\u8be2\u957f\u5ea6\u4ee5\u53ca\u8986\u76d6\u6bd4\u4f8b\u3002\u56db\u4e2a\u8f93\u51fa\u91cf\u5404\u6709\u542b\u4e49\uff0c\u4e0d\u80fd\u53ea\u56e0\u4e3a\u90fd\u6765\u81ea\u540c\u4e00\u884c\uff0c\u5c31\u5c06\u547d\u4e2d\u6570\u5f53\u6df1\u5ea6\u3001\u5c06\u957f\u5ea6\u5f53\u6bd4\u4f8b\u3002<\/p>\n
\n\n\n\n\n\n\n\n\n
\u67e5\u8be2<\/th>\n\u6ce8\u91ca\u547d\u4e2d\u6570<\/th>\n\u975e\u91cd\u590d\u8986\u76d6\u957f\u5ea6<\/th>\n\u8986\u76d6\u6bd4\u4f8b<\/th>\n<\/tr>\n<\/thead>\n
\u7532<\/td>\n3<\/td>\n100<\/td>\n100%<\/td>\n<\/tr>\n
\u4e59<\/td>\n2<\/td>\n100<\/td>\n100%<\/td>\n<\/tr>\n
\u4e19<\/td>\n1<\/td>\n10<\/td>\n10%<\/td>\n<\/tr>\n
\u4e01<\/td>\n0<\/td>\n0<\/td>\n0%<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
bedtools intersect -a A.bed -b B.bed -wo\r\nbedtools coverage -a A.bed -b B.bed\r\n<\/code><\/pre>\n
\u524d\u4e00\u6761\u4fbf\u4e8e\u8ffd\u6eaf\u6bcf\u4e00\u5bf9\u91cd\u53e0\u7684\u6765\u6e90\uff0c\u540e\u4e00\u6761\u56de\u7b54\u67e5\u8be2\u672c\u8eab\u6709\u591a\u5c11\u4f4d\u7f6e\u88ab\u8986\u76d6\u3002\u5047\u5982\u4f60\u7684\u7814\u7a76\u95ee\u9898\u662f\u201c\u542f\u52a8\u5b50\u88ab\u67d0\u7c7b\u72b6\u6001\u8986\u76d6\u7684\u6bd4\u4f8b\u201d\uff0c\u5e94\u4f18\u5148\u660e\u786e\u662f\u5426\u9700\u8981\u533a\u95f4\u5e76\u96c6\u610f\u4e49\u4e0a\u7684\u8986\u76d6\u3002\u5982\u679c\u95ee\u9898\u662f\u201c\u6bcf\u4e2a\u542f\u52a8\u5b50\u5bf9\u5e94\u591a\u5c11\u6761\u6ce8\u91ca\u8bb0\u5f55\u201d\uff0c\u5219\u53ef\u4ee5\u8ba1\u7b97\u5339\u914d\u6570\uff0c\u4f46\u8981\u8bf4\u660e\u540c\u4e00\u57fa\u56e0\u7684\u591a\u4e2a\u8f6c\u5f55\u672c\u662f\u5426\u7b97\u591a\u4e2a\u8bb0\u5f55\u3002<\/p>\n
\u8fd9\u91cc\u4e5f\u53ef\u4ee5\u5f62\u6210\u4e00\u4e2a\u7b80\u5355\u7684\u8d28\u63a7\u89c4\u5219\u3002\u5bf9\u4e8e\u975e\u91cd\u590d\u8986\u76d6\u6bd4\u4f8b\uff0c\u7ed3\u679c\u4e0d\u5e94\u8d85\u8fc7\u4e00\u3002\u82e5\u51fa\u73b0\u5927\u4e8e\u4e00\u7684\u6570\u503c\uff0c\u5148\u68c0\u67e5\u662f\u5426\u628a\u6bcf\u5bf9\u5339\u914d\u7684\u91cd\u53e0\u957f\u5ea6\u7d2f\u52a0\uff0c\u518d\u9664\u4ee5\u67e5\u8be2\u957f\u5ea6\u3002\u4e0d\u8981\u6025\u7740\u622a\u65ad\u5230\u4e00\uff0c\u56e0\u4e3a\u622a\u65ad\u53ea\u4f1a\u9690\u85cf\u91cd\u590d\u7d2f\u8ba1\uff0c\u8ba9\u9519\u8bef\u7edf\u8ba1\u53e3\u5f84\u7ee7\u7eed\u8fdb\u5165\u4e0b\u4e00\u6b65\u3002<\/p>\n
\u56db\u3001\u8986\u76d6\u516b\u6210\u7684\u95e8\u69db\uff0c\u5230\u5e95\u65bd\u52a0\u5728\u8c01\u8eab\u4e0a<\/h2>\n
\u6700\u5bb9\u6613\u6df7\u6dc6\u7684\u662f\u5355\u6b21\u5339\u914d\u6bd4\u4f8b\u4e0e\u603b\u8986\u76d6\u6bd4\u4f8b\u3002\u7532\u7684\u6ce8\u91ca\u5e76\u96c6\u8986\u76d6\u767e\u5206\u4e4b\u767e\uff0c\u4f46\u4efb\u4f55\u4e00\u6761\u6ce8\u91ca\u5bf9\u7532\u7684\u8986\u76d6\u90fd\u6ca1\u6709\u8fbe\u5230\u516b\u6210\u3002\u672c\u6b21\u5c06\u6700\u5c0f\u6bd4\u4f8b\u8bbe\u4e3a\u516b\u6210\u540e\uff0c\u7532\u7684\u5408\u683c\u5339\u914d\u6570\u53d8\u6210\u96f6\u3002\u4e59\u4e5f\u4e00\u6837\uff0c\u4e24\u6761\u5404\u8986\u76d6\u4e00\u534a\u7684\u6ce8\u91ca\u5408\u8d77\u6765\u8986\u76d6\u5168\u90e8\uff0c\u5374\u6ca1\u6709\u4efb\u4f55\u5355\u6761\u8fbe\u5230\u516b\u6210\u3002<\/p>\n
bedtools intersect -a A.bed -b B.bed -f 0.8 -c\r\nbedtools intersect -a short.bed -b long.bed -f 0.9 -u\r\nbedtools intersect -a short.bed -b long.bed -f 0.9 -r -u\r\n<\/code><\/pre>\n
\u7b2c\u4e00\u6761\u547d\u4ee4\u5728\u672c\u4f8b\u8fd4\u56de\u56db\u4e2a\u96f6\u3002\u5b83\u5e76\u6ca1\u6709\u5426\u5b9a\u524d\u9762\u7684\u767e\u5206\u4e4b\u767e\u8986\u76d6\uff0c\u800c\u662f\u5bf9\u6bcf\u4e00\u5bf9\u5019\u9009\u5339\u914d\u5355\u72ec\u5e94\u7528\u95e8\u69db\u3002\u5982\u679c\u9700\u6c42\u662f\u6ce8\u91ca\u5e76\u96c6\u8986\u76d6\u67e5\u8be2\u81f3\u5c11\u516b\u6210\uff0c\u5e94\u5148\u8ba1\u7b97\u8986\u76d6\u6bd4\u4f8b\uff0c\u518d\u6309\u8be5\u6bd4\u4f8b\u7b5b\u9009\u3002\u82e5\u4e1a\u52a1\u5141\u8bb8\u5148\u5408\u5e76\u6ce8\u91ca\u533a\u95f4\uff0c\u4e5f\u9700\u8981\u786e\u8ba4\u5408\u5e76\u662f\u5426\u4f1a\u4e22\u6389\u57fa\u56e0\u3001\u7c7b\u522b\u6216\u94fe\u65b9\u5411\u7b49\u9700\u8981\u533a\u5206\u7684\u4fe1\u606f\u3002<\/p>\n
\u540e\u4e24\u6761\u7528\u72ec\u7acb\u7684\u957f\u77ed\u533a\u95f4\u68c0\u9a8c\u5206\u6bcd\u3002\u77ed\u533a\u95f4\u4e3a 100 \u5230 200\uff0c\u957f\u533a\u95f4\u4e3a 0 \u5230 1000\u3002\u77ed\u533a\u95f4\u5b8c\u5168\u4f4d\u4e8e\u957f\u533a\u95f4\u5185\uff0c\u56e0\u6b64\u53ea\u8981\u6c42\u77ed\u533a\u95f4\u88ab\u8986\u76d6\u4e5d\u6210\u65f6\u80fd\u591f\u4fdd\u7559\u3002\u52a0\u5165\u53cc\u5411\u6bd4\u4f8b\u8981\u6c42\u540e\u6ca1\u6709\u8f93\u51fa\uff0c\u56e0\u4e3a\u540c\u6837\u7684\u4e00\u767e\u78b1\u57fa\u53ea\u5360\u957f\u533a\u95f4\u7684\u5341\u5206\u4e4b\u4e00\u3002<\/p>\n
\u9009\u62e9\u5355\u5411\u8fd8\u662f\u53cc\u5411\u6761\u4ef6\uff0c\u53d6\u51b3\u4e8e\u8981\u5224\u65ad\u201c\u843d\u5728\u8f83\u5927\u533a\u57df\u5185\u201d\u8fd8\u662f\u201c\u4e24\u4e2a\u533a\u57df\u8303\u56f4\u63a5\u8fd1\u201d\u3002\u7a84\u5cf0\u4e0e\u5927\u578b\u8c03\u63a7\u533a\u76f8\u4ea4\u65f6\uff0c\u53cc\u5411\u4e25\u683c\u95e8\u69db\u53ef\u80fd\u4e22\u6389\u539f\u672c\u7b26\u5408\u95ee\u9898\u5b9a\u4e49\u7684\u8bb0\u5f55\u3002\u6bd4\u8f83\u4e24\u4e2a\u5cf0\u8c03\u7528\u7ed3\u679c\u7684\u8fb9\u754c\u4e00\u81f4\u6027\u65f6\uff0c\u5355\u5411\u5b8c\u5168\u5305\u542b\u53c8\u53ef\u80fd\u663e\u5f97\u8fc7\u4e8e\u5bbd\u677e\u3002\u95e8\u69db\u5e94\u7531\u6bd4\u8f83\u76ee\u7684\u89e3\u91ca\uff0c\u800c\u4e0d\u662f\u53ea\u51ed\u6570\u503c\u770b\u8d77\u6765\u4e25\u683c\u3002<\/p>\n
\u4e94\u3001\u94fe\u65b9\u5411\u6539\u53d8\u7684\u4e0d\u53ea\u662f\u884c\u6570<\/h2>\n
\u672c\u4f8b\u7532\u7684\u4e09\u6761\u5339\u914d\u4e2d\uff0c\u524d\u4e24\u6761\u662f\u6b63\u94fe\uff0c\u7b2c\u4e09\u6761\u662f\u8d1f\u94fe\u3002\u9650\u5236\u540c\u94fe\u540e\uff0c\u7532\u4fdd\u7559\u4e24\u6761\u5339\u914d\uff0c\u975e\u91cd\u590d\u8986\u76d6\u957f\u5ea6\u4ece\u4e00\u767e\u964d\u5230\u516b\u5341\u3002\u4e59\u4fdd\u7559\u4e00\u6761\u8d1f\u94fe\u5339\u914d\uff0c\u8986\u76d6\u4ece\u4e00\u767e\u964d\u5230\u4e94\u5341\u3002\u4e19\u53ea\u6709\u53cd\u94fe\u6ce8\u91ca\uff0c\u540c\u94fe\u6761\u4ef6\u4e0b\u8986\u76d6\u53d8\u6210\u96f6\u3002<\/p>\n
\u8fd9\u79cd\u53d8\u5316\u4e3a\u68c0\u67e5\u5b9e\u9a8c\u8bbe\u8ba1\u63d0\u4f9b\u4e86\u4e00\u4e2a\u53ef\u89c1\u4f8b\u5b50\u3002\u5982\u679c\u67e5\u8be2\u8868\u8fbe\u7684\u662f\u5177\u6709\u65b9\u5411\u6027\u7684\u8f6c\u5f55\u4e8b\u4ef6\uff0c\u5ffd\u7565\u94fe\u53ef\u80fd\u628a\u53cd\u5411\u91cd\u53e0\u7b97\u4f5c\u652f\u6301\u8bc1\u636e\u3002\u5982\u679c\u67e5\u8be2\u53ea\u662f\u65e0\u65b9\u5411\u7684\u5f00\u653e\u67d3\u8272\u8d28\u533a\u95f4\uff0c\u673a\u68b0\u5957\u7528\u94fe\u6761\u4ef6\u53c8\u53ef\u80fd\u6392\u9664\u672c\u5e94\u4fdd\u7559\u7684\u4f4d\u7f6e\u5173\u7cfb\u3002\u4e0d\u80fd\u56e0\u4e3a\u8f93\u5165\u6587\u4ef6\u6070\u597d\u6709\u7b2c\u516d\u5217\uff0c\u5c31\u9ed8\u8ba4\u8fd9\u4e00\u5217\u5177\u5907\u9002\u7528\u4e8e\u5f53\u524d\u5206\u6790\u7684\u65b9\u5411\u542b\u4e49\u3002<\/p>\n
\u8fd8\u9700\u8981\u533a\u5206\u57fa\u56e0\u6ce8\u91ca\u7684\u94fe\u3001\u6bd4\u5bf9\u8bb0\u5f55\u7684\u94fe\u548c\u6587\u5e93\u534f\u8bae\u5bf9\u5e94\u7684\u8f6c\u5f55\u65b9\u5411\u3002\u5b83\u4eec\u5e76\u4e0d\u5728\u6240\u6709\u6d4b\u5e8f\u65b9\u6848\u4e2d\u90fd\u4e00\u4e00\u76f8\u540c\u3002\u672c\u6b21\u4f7f\u7528\u7684\u662f\u6211\u4eec\u81ea\u5df1\u5199\u5165\u7684\u65b9\u5411\u6807\u7b7e\uff0c\u5df2\u7ecf\u8db3\u591f\u9a8c\u8bc1\u533a\u95f4\u5de5\u5177\u5982\u4f55\u6267\u884c\u6761\u4ef6\uff0c\u4f46\u4e0d\u80fd\u9a8c\u8bc1\u771f\u5b9e\u6587\u5e93\u7684\u94fe\u7279\u5f02\u6027\u3002\u771f\u5b9e\u6570\u636e\u5e94\u5148\u501f\u52a9\u5df2\u77e5\u57fa\u56e0\u6216\u4e13\u95e8\u8d28\u63a7\u6838\u5b9e\u65b9\u5411\u7ea6\u5b9a\u3002<\/p>\n
\u516d\u3001\u76f8\u4ea4\u3001\u5408\u5e76\u548c\u8f6c\u5f55\u672c\u5206\u5757\uff0c\u4e0d\u80fd\u4e92\u76f8\u66ff\u4ee3<\/h2>\n
\u7532\u4e0e\u4e59\u6ca1\u6709\u5171\u540c\u78b1\u57fa\uff0c\u4f46\u662f\u9ed8\u8ba4\u5408\u5e76\u64cd\u4f5c\u628a\u5b83\u4eec\u5408\u6210 100 \u5230 300 \u7684\u8fde\u7eed\u533a\u95f4\u3002\u8fd9\u5e76\u4e0d\u77db\u76fe\u3002\u76f8\u4ea4\u8981\u6c42\u5171\u4eab\u4f4d\u7f6e\uff0c\u9ed8\u8ba4\u5408\u5e76\u5219\u5141\u8bb8\u8fb9\u754c\u76f8\u63a5\u3002\u6211\u4eec\u901a\u8fc7\u9644\u52a0\u540d\u79f0\u4e0e\u65b9\u5411\u6c47\u603b\u4fdd\u7559\u4e86\u6765\u6e90\uff0c\u8f93\u51fa\u660e\u786e\u5217\u51fa\u7532\u548c\u4e59\uff0c\u4ee5\u53ca\u6b63\u8d1f\u4e24\u4e2a\u65b9\u5411\u3002<\/p>\n
\u9650\u5236\u540c\u94fe\u5408\u5e76\u540e\uff0c\u7532\u4e0e\u4e59\u4fdd\u6301\u5206\u5f00\u3002\u8fd9\u4e2a\u5bf9\u7167\u5c24\u5176\u9002\u5408\u68c0\u67e5\u201c\u5148\u5408\u5e76\u5168\u90e8\u6ce8\u91ca\uff0c\u518d\u7b97\u8986\u76d6\u201d\u7684\u505a\u6cd5\u662f\u5426\u7b26\u5408\u9700\u6c42\u3002\u5408\u5e76\u540e\u7684\u4e00\u4e2a\u5927\u533a\u95f4\u53ea\u8868\u793a\u7a7a\u95f4\u4e0a\u8fde\u7eed\uff0c\u4e0d\u80fd\u636e\u6b64\u65ad\u8a00\u5176\u5185\u90e8\u5c5e\u4e8e\u540c\u4e00\u57fa\u56e0\u3001\u540c\u4e00\u5cf0\u4e8b\u4ef6\u6216\u540c\u4e00\u79cd\u8c03\u63a7\u72b6\u6001\u3002\u9700\u8981\u4fdd\u7559\u6765\u6e90\u65f6\uff0c\u5e94\u8be5\u660e\u786e\u9009\u62e9\u6c47\u603b\u5b57\u6bb5\uff0c\u5e76\u68c0\u67e5\u6c47\u603b\u7ed3\u679c\u662f\u5426\u4ecd\u80fd\u56de\u7b54\u539f\u95ee\u9898\u3002<\/p>\n
bedtools merge -i A.bed -c 4,6 -o distinct\r\nbedtools merge -i A.bed -s -c 4,6 -o distinct\r\nbedtools intersect -a transcript.bed -b intron.bed -u\r\nbedtools intersect -a transcript.bed -b intron.bed -split -u\r\n<\/code><\/pre>\n
\u8f6c\u5f55\u672c\u4f8b\u5b50\u8fdb\u4e00\u6b65\u8bf4\u660e\u4e86\u201c\u533a\u95f4\u7684\u5185\u90e8\u7ed3\u6784\u201d\u3002\u6211\u4eec\u5199\u5165\u4e00\u4e2a\u4ece 100 \u5230 400 \u7684\u4e24\u5757\u8f6c\u5f55\u672c\uff0c\u4e24\u4e2a\u5916\u663e\u5b50\u5206\u522b\u4f4d\u4e8e 100 \u5230 150\u3001350 \u5230 400\uff0c\u53e6\u653e\u4e00\u4e2a\u4f4d\u4e8e 250 \u5230 260 \u7684\u67e5\u8be2\u3002\u6309\u6574\u4e2a\u8de8\u5ea6\u5224\u65ad\u65f6\uff0c\u4e24\u8005\u76f8\u4ea4\u3002\u6309\u5206\u5757\u5224\u65ad\u65f6\uff0c\u6ca1\u6709\u76f8\u4ea4\uff0c\u56e0\u4e3a\u67e5\u8be2\u5b8c\u5168\u4f4d\u4e8e\u4e24\u5757\u4e4b\u95f4\u3002<\/p>\n
\u56e0\u6b64\uff0c\u60f3\u7edf\u8ba1\u5916\u663e\u5b50\u8986\u76d6\uff0c\u5c31\u5fc5\u987b\u8ba9\u8f93\u5165\u7ed3\u6784\u548c\u547d\u4ee4\u5171\u540c\u8868\u8fbe\u5916\u663e\u5b50\u3002\u4ec5\u628a\u8f6c\u5f55\u672c\u603b\u8d77\u6b62\u5750\u6807\u5f53\u4f5c\u666e\u901a\u4e09\u5217\u533a\u95f4\uff0c\u5df2\u7ecf\u4e22\u6389\u4e86\u5185\u90e8\u65ad\u5f00\u7684\u4fe1\u606f\u3002\u53cd\u8fc7\u6765\uff0c\u5982\u679c\u7814\u7a76\u7684\u662f\u6574\u4e2a\u57fa\u56e0\u5ea7\u8303\u56f4\uff0c\u5206\u5757\u540e\u53ea\u68c0\u67e5\u5916\u663e\u5b50\u4e5f\u53ef\u80fd\u6539\u53d8\u95ee\u9898\u3002\u8f6f\u4ef6\u4e0d\u4f1a\u66ff\u6211\u4eec\u9009\u62e9\u8fd9\u4e24\u4e2a\u751f\u7269\u5b66\u5bf9\u8c61\u3002<\/p>\n
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\u4e0b\u8f7d\u672c\u7ec4\u4e09\u7bc7\u590d\u73b0\u811a\u672c\u4e0e\u5b9e\u6d4b\u8bb0\u5f55<\/a> \u540e\uff0c\u5728\u6709 Docker \u7684 Linux \u73af\u5883\u8fdb\u5165\u672c\u5de5\u5177\u76ee\u5f55\uff0c\u6267\u884c\u4e0b\u9762\u7684\u547d\u4ee4\u3002\u811a\u672c\u4f7f\u7528\u56fa\u5b9a\u955c\u50cf\u6458\u8981\uff0c\u91cd\u5efa\u6240\u6709\u5c0f\u6587\u4ef6\uff0c\u5e76\u8bb0\u5f55\u6210\u529f\u64cd\u4f5c\u53ca\u6545\u610f\u5236\u9020\u7684\u6392\u5e8f\u5931\u8d25\u3002\u8bfb\u53d6\u7ed3\u679c\u65f6\uff0c\u5e94\u6838\u5bf9\u5177\u4f53\u6848\u4f8b\u7684\u9884\u671f\u9000\u51fa\u7801\uff0c\u4e0d\u5e94\u628a\u6240\u6709\u975e\u96f6\u7801\u7edf\u4e00\u89e3\u91ca\u4e3a\u73af\u5883\u5b89\u88c5\u5931\u8d25\u3002<\/p>\n
python3 run.py output\r\n<\/code><\/pre>\n
\u53c2\u6570\u5b9a\u4e49\u53ef\u5bf9\u7167 intersect \u5b98\u65b9\u6587\u6863<\/a>\u3001coverage \u5b98\u65b9\u6587\u6863<\/a> \u4e0e merge \u5b98\u65b9\u6587\u6863<\/a>\u3002\u672c\u6587\u7684\u5750\u6807\u3001\u7edf\u8ba1\u8868\u4e0e\u5bf9\u7167\u7ed3\u679c\u5747\u7531\u968f\u6587\u811a\u672c\u6784\u9020\u548c\u5b9e\u9645\u6267\u884c\uff0c\u9002\u5408\u5b66\u4e60\u4e0e\u68c0\u67e5\u8bed\u4e49\uff0c\u4e0d\u4ee3\u8868\u771f\u5b9e\u6570\u636e\u7684\u5206\u6790\u7ed3\u8bba\u3002<\/p>\n
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