{"id":21125,"date":"2023-12-19T16:08:20","date_gmt":"2023-12-19T08:08:20","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=21125"},"modified":"2023-12-19T16:08:23","modified_gmt":"2023-12-19T08:08:23","slug":"21125","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=21125","title":{"rendered":""},"content":{"rendered":"

\u5f3a\u5927\u7684\u57fa\u56e0\u7b97\u6cd5\u5de5\u5177\u5927\u5e08\uff1abedtools<\/strong><\/p>\n

hello\uff0c\u4f60\u77e5\u9053\u6709\u4e00\u4e2a\u5f3a\u5927\u7684\u57fa\u56e0\u7ec4\u7b97\u6cd5\u5de5\u5177\u96c6\u561b\uff1f\u5b83\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u5904\u7406\u57fa\u56e0\u7ec4\u4e2d\u751f\u6210\u7684\u4e00\u7cfb\u5217bed\u3001bam\u7b49\u683c\u5f0f\u7684\u6587\u4ef6\uff0c\u60f3\u77e5\u9053\u5177\u4f53\u5982\u4f55\u64cd\u4f5c\u561b\uff1f\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u770b\u4e0b\u53bb\u5427\uff01<\/p>\n

\u4ec0\u4e48\u662fbedtools\uff1f<\/strong><\/p>\n

Bedtools \u662f\u4e00\u4e2a\u7528\u4e8e\u57fa\u56e0\u7ec4\u6570\u636e\u5206\u6790\u7684\u5f3a\u5927\u5de5\u5177\u96c6\uff0c\u5e7f\u6cdb\u5e94\u7528\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u548c\u57fa\u56e0\u7ec4\u5b66\u9886\u57df\u3002\u5b83\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u7528\u4e8e\u5904\u7406 BED\uff08Browser Extensible Data\uff09\u683c\u5f0f\u6587\u4ef6\u7684\u547d\u4ee4\u884c\u5de5\u5177\uff0c\u53ef\u4ee5\u9ad8\u6548\u5730\u8fdb\u884c\u57fa\u56e0\u7ec4\u533a\u57df\u64cd\u4f5c\u3001\u91cd\u53e0\u5206\u6790\u3001\u6bd4\u8f83\u548c\u6ce8\u91ca\u7b49\u64cd\u4f5c\u3002<\/p>\n

Bedtools \u652f\u6301\u5404\u79cd\u5e38\u89c1\u7684\u57fa\u56e0\u7ec4\u64cd\u4f5c\uff0c\u5305\u62ec\u5e76\u96c6\u3001\u4ea4\u96c6\u3001\u5dee\u96c6\u3001\u5408\u5e76\u3001\u6392\u5e8f\u3001\u8fc7\u6ee4\u7b49\u3002\u901a\u8fc7\u8fd9\u4e9b\u64cd\u4f5c\uff0c\u7528\u6237\u53ef\u4ee5\u5c06\u4e0d\u540c\u7684\u57fa\u56e0\u7ec4\u533a\u57df\u6587\u4ef6\u8fdb\u884c\u7ec4\u5408\u3001\u7b5b\u9009\u548c\u6bd4\u8f83\uff0c\u4ece\u800c\u5b9e\u73b0\u5bf9\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u8be6\u7ec6\u5206\u6790\u548c\u6ce8\u91ca\u3002<\/p>\n

Bedtools \u8fd8\u53ef\u4ee5\u8fdb\u884c\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u91cd\u53e0\u5206\u6790\u3002\u901a\u8fc7\u8ba1\u7b97\u4e24\u4e2a\u6216\u591a\u4e2a\u533a\u57df\u6587\u4ef6\u4e4b\u95f4\u7684\u91cd\u53e0\u60c5\u51b5\uff0c\u53ef\u4ee5\u786e\u5b9a\u57fa\u56e0\u6216\u5176\u4ed6\u529f\u80fd\u5143\u4ef6\u5728\u57fa\u56e0\u7ec4\u4e0a\u7684\u4f4d\u7f6e\u5173\u7cfb\uff0c\u5e76\u8fdb\u4e00\u6b65\u7814\u7a76\u5b83\u4eec\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u3002<\/p>\n

\u9664\u4e86\u57fa\u672c\u7684\u64cd\u4f5c\u548c\u91cd\u53e0\u5206\u6790\uff0cBedtools \u8fd8\u63d0\u4f9b\u4e86\u4e00\u4e9b\u9ad8\u7ea7\u529f\u80fd\uff0c\u4f8b\u5982\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u7a81\u53d8\u5206\u6790\u3001\u7edf\u8ba1\u5206\u6790\u4ee5\u53ca\u57fa\u56e0\u7ec4\u529f\u80fd\u6ce8\u91ca\u7b49\u3002\u8fd9\u4f7f\u5f97 Bedtools \u6210\u4e3a\u4e86\u751f\u7269\u5b66\u7814\u7a76\u4e2d\u4e0d\u53ef\u6216\u7f3a\u7684\u5de5\u5177\u4e4b\u4e00\u3002<\/p>\n

\u603b\u4e4b\uff0cBedtools \u662f\u4e00\u4e2a\u529f\u80fd\u5f3a\u5927\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u5904\u7406\u5de5\u5177\u96c6\uff0c\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u8fdb\u884c\u5404\u79cd\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u64cd\u4f5c\u3001\u5206\u6790\u548c\u6ce8\u91ca\uff0c\u4e3a\u57fa\u56e0\u7ec4\u5b66\u548c\u751f\u7269\u4fe1\u606f\u5b66\u7814\u7a76\u63d0\u4f9b\u4e86\u91cd\u8981\u7684\u652f\u6301\u3002<\/p>\n

bedtools\u5904\u7406bed\u6587\u4ef6<\/strong><\/p>\n

bedtools\u5728\u5904\u7406\u4e00\u7cfb\u5217bed\u6587\u4ef6\u65f6\uff0c\u6839\u636e\u4e0d\u540c\u7684\u9700\u6c42\u6709\u4e0d\u540c\u7684\u547d\u4ee4\uff0c\u63a5\u4e0b\u6765\u5c0f\u679c\u5148\u4e3a\u5927\u5bb6\u4ecb\u7ecd\u4e94\u79cd\u6700\u5e38\u89c1\u7684\u64cd\u4f5c\u3002\u5728\u8fd9\u91cc\u6211\u4eec\u5148\u5f15\u5165\u4e09\u4e2a\u793a\u4f8b\u6587\u4ef6\uff1a<\/p>\n

1.new-chr.bed<\/p>\n

2.newArea.bed<\/p>\n

3.newGene.bed<\/p>\n

\u4ee5\u62df\u5357\u82a5\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u4e3a\u57fa\u7840\uff0cnew-chr.bed\u4ee3\u8868\u62df\u5357\u82a5\u57fa\u56e0\u7ec4\u4e0a7\u6761\u5e8f\u5217\u7684\u957f\u5ea6\u533a\u95f4\uff0cnewArea.bed\u4ee3\u8868\u6211\u4eec\u901a\u8fc7\u6bd4\u5bf9\u8f6f\u4ef6\u6bd4\u5bf9\u540e\u4ea7\u751f\u7684\u533a\u95f4\u5408\u96c6\u6587\u4ef6\uff0cnewGene.bed\u4ee3\u8868\u6211\u4eec\u4ece\u62df\u5357\u82a5\u57fa\u56e0\u7ec4\u7684\u6ce8\u91ca\u6587\u4ef6\u4e2d\u63d0\u53d6\u51fa\u7684\u57fa\u56e0\u4fe1\u606f\u533a\u95f4\u6587\u4ef6\u3002\u8fd9\u91cc\u7684bed\u6587\u4ef6\u4ec5\u4f9b\u8bf4\u660e\u5de5\u5177\u7684\u529f\u80fd\uff0c\u5927\u5bb6\u5728\u5b66\u4e60\u65f6\u8981\u7075\u6d3b\u66ff\u6362\u6210\u81ea\u5df1\u7684\u6587\u4ef6\u54e6\uff01<\/p>\n

\u5bf9\u6587\u4ef6\u6392\u5e8f<\/strong><\/p>\n

\u5f53\u6211\u4eec\u62ff\u5230\u4e00\u4e2a\u533a\u95f4\u6587\u4ef6\u65f6\uff0c\u53ea\u6709\u5c06\u5176\u6392\u5e8f\u597d\u624d\u80fd\u4fdd\u8bc1\u540e\u7eed\u7684\u64cd\u4f5c\u66f4\u52a0\u51c6\u786e\uff0c\u6240\u4ee5\u6392\u5e8f\u8fd9\u4e00\u64cd\u4f5c\u5f80\u5f80\u662f\u5904\u7406bed\u6587\u4ef6\u7684\u7b2c\u4e00\u6b65\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u6765\u8fdb\u884c\u6392\u5e8f\u64cd\u4f5c\uff1a<\/p>\n

bedtools sort -i newArea.bed > newSort.bed<\/p>\n

\u6392\u5e8f\u540e\uff0c\u4f60\u5c06\u5f97\u5230\u4e00\u4e2a\u6392\u5e8f\u597d\u7684\u533a\u95f4\u6587\u4ef6\uff1a<\/p>\n

<\/strong><\/p>\n

\u5408\u5e76\u76f8\u540c\u533a\u95f4<\/strong><\/p>\n

\u5f53\u4f60\u6392\u5e8f\u5b8c\u6210\u540e\uff0c\u6709\u65f6\u6211\u4eec\u7684\u533a\u95f4\u4e2d\u6709\u5f88\u591a\u201c\u91cd\u590d\u201d\u7684\u533a\u95f4\uff0c\u5408\u5e76\u76f8\u540c\u4ee5\u53ca\u91cd\u53e0\u7684\u533a\u95f4\u53ef\u4ee5\u5e2e\u52a9\u7b80\u5316\u6211\u4eec\u7684\u533a\u95f4\uff0c\u8ba9\u6570\u636e\u66f4\u76f4\u89c2\u4ee5\u53ca\u7b80\u6d01\uff0c\u4f60\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u6765\u5b8c\u6210\u5408\u5e76\u64cd\u4f5c\uff1a<\/p>\n

bedtools merge -i newSort.bed > newMerge.ned<\/p>\n

\u5408\u5e76\u540e\u7684\u6587\u4ef6\u683c\u5f0f\u5982\u4e0b\uff1a<\/p>\n

<\/strong><\/p>\n

\u6c42\u533a\u95f4\u7684\u8986\u76d6\u5ea6<\/strong><\/p>\n

\u5f53\u4f60\u60f3\u6c42B\u6587\u4ef6\u5728A\u6587\u4ef6\u4e0a\u7684\u533a\u95f4\u8986\u76d6\u5ea6\u65f6\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n

bedtools coverage -a A.bed -b B.bed > C.bed
\neg:
\nbedtools coverage -a new-chr.bed -b newMerge.bed > newOnChr.bed<\/p>\n

\u5c0f\u679c\u6e29\u99a8\u63d0\u793a\uff1a\u5728\u8fd9\u91cc\uff0c-a\u548c-b\u540e\u5206\u522b\u8f93\u5165\u4e24\u4e2a\u533a\u95f4\u6587\u4ef6\uff0c\u5176\u4e2d-a\u540e\u7684\u6587\u4ef6\u53c2\u6570\u8981\u8bbe\u7f6e\u4e3a\u4e24\u4e2a\u533a\u95f4\u6587\u4ef6\u4e2d\u8303\u56f4\u5927\u7684\u6587\u4ef6\u54e6\u3002<\/p>\n

\u8fd0\u884c\u540e\u5f97\u5230\u7684\u7ed3\u679c\u5982\u4e0b\uff1a<\/p>\n

<\/strong><\/p>\n

\u6c42\u4e24\u4e2a\u533a\u95f4\u7684\u4ea4\u96c6<\/strong><\/p>\n

\u5f53\u8981\u6c42\u4e24\u4e2a\u533a\u95f4\u6587\u4ef6\u7684\u4ea4\u96c6\u533a\u95f4\u65f6\uff0c\u4f60\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4<\/p>\n

bedtools intersect -a A.bed -b B.bed > C.bed
\neg:
\nbedtools intersect -a newSort.bed -b newGene.bed > newAndGene.bed<\/p>\n

\u6700\u540e\u5f97\u5230\u7684\u7ed3\u679c\u5982\u4e0b\uff1a<\/p>\n

<\/p>\n

\u6c42\u4e24\u4e2a\u533a\u95f4\u7684\u5dee\u96c6<\/strong><\/p>\n

\u5f53\u8981\u6c42\u4e24\u4e2a\u533a\u95f4\u7684\u5dee\u96c6\u65f6\uff0c\u6211\u4eec\u9700\u8981\u7528\u5230\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n

bedtools subtract -a A.bed -b B.bed > C.bed
\n\u200b
\neg\uff1a
\nbedtools subtract -a newSort.bed -b newGene.bed > newNoGene.bed<\/p>\n

\u6ce8\u610f\uff0c\u4ee5\u4e0a\u547d\u4ee4\u6c42\u5f97\u7684\u65f6A.bed\u6587\u4ef6\u4e2d\u53bb\u9664\u4e86B.bed\u6587\u4ef6\u4e2d\u7684\u533a\u95f4\u5269\u4f59\u7684\u533a\u95f4\u6587\u4ef6\uff0c\u793a\u4f8b\u6587\u4ef6\u8fd0\u884c\u540e\u7684\u7ed3\u679c\u5982\u4e0b\uff1a<\/p>\n

<\/p>\n

\u4ee5\u4e0a\u5c31\u662fbedtools\u6700\u5e38\u7528\u7684\u4e94\u4e2a\u529f\u80fd\uff0c\u8fd8\u6709\u5f88\u591a\u4e30\u5bcc\u7684\u529f\u80fd\u7b49\u5f85\u4f60\u7ee7\u7eed\u63a2\u7d22\uff0c\u600e\u4e48\u6837\uff0c\u662f\u4e0d\u662f\u5f88\u7b80\u5355\uff1f\u8d76\u5feb\u62ff\u8d77\u4f60\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u7ec3\u8d77\u6765\u5427\uff01\u66f4\u591a\u5b66\u4e60\u5e72\u8d27\u8981\u7ee7\u7eed\u5173\u6ce8\u5c0f\u679c\u54e6\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"

\u5f3a\u5927\u7684\u57fa\u56e0\u7b97\u6cd5\u5de5\u5177\u5927\u5e08\uff1abedtools hello\uff0c\u4f60\u77e5\u9053\u6709\u4e00\u4e2a\u5f3a\u5927\u7684\u57fa\u56e0\u7ec4\u7b97\u6cd5\u5de5\u5177\u96c6\u561b\uff1f\u5b83\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u5904\u7406 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/21125"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=21125"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/21125\/revisions"}],"predecessor-version":[{"id":21131,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/21125\/revisions\/21131"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21125"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21125"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21125"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}