{"id":24275,"date":"2024-01-11T17:00:15","date_gmt":"2024-01-11T09:00:15","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24275"},"modified":"2024-01-11T17:00:17","modified_gmt":"2024-01-11T09:00:17","slug":"%e5%bc%ba%e5%8a%9b%e6%8e%a8%e8%8d%90%ef%bc%81hic-pro-homer%e5%ae%9e%e7%8e%b0%e4%b8%89%e7%bb%b4%e5%9f%ba%e5%9b%a0%e7%bb%84ab%e5%8c%ba%e5%ae%a4%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24275","title":{"rendered":"\u5f3a\u529b\u63a8\u8350\uff01HiC-Pro + homer\u5b9e\u73b0\u4e09\u7ef4\u57fa\u56e0\u7ec4AB\u533a\u5ba4\u5206\u6790"},"content":{"rendered":"

\u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u53c8\u8ddf\u5927\u5bb6\u89c1\u9762\u5566\uff01\u8fd9\u6b21\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u4e09\u7ef4\u57fa\u56e0\u7ec4\u7684AB\u533a\u5ba4\u5206\u6790\u7684\u5185\u5bb9<\/p>\n

\u4ee5\u9632\u5c0f\u4f19\u4f34\u4eec\u8ddf\u4e0d\u4e0a\u5c0f\u679c\u7684\u8282\u594f\uff0c\u5c0f\u679c\u9996\u5148\u8ddf\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e0b\u4e09\u7ef4\u57fa\u56e0\u7ec4\u7684\u4e00\u4e9b\u76f8\u5173\u6982\u5ff5\uff1a<\/p>\n

    \n
  1. \u5728\u771f\u6838\u751f\u7269\u7684\u57fa\u56e0\u7ec4\u4e2d\uff0c\u7ec6\u80de\u6838\u5185\u7684\u67d3\u8272\u8d28\u5206\u5e03\u5e76\u4e0d\u662f\u968f\u673a\u7684\uff0c\u4e3a\u4e86\u8de8\u8d8a\u8f83\u5927\u7684\u57fa\u56e0\u7ec4\u7684\u8ddd\u79bb\u53bb\u76f8\u4e92\u4f5c\u7528\uff0c\u4f8b\u5982\u589e\u5f3a\u5b50\u548c\u542f\u52a8\u5b50\u7684\u4e92\u4f5c\uff0c\u8fd9\u4e9b\u5bc6\u5207\u4f5c\u7528\u7684\u67d3\u8272\u8d28\u4f1a\u9760\u7684\u66f4\u8fd1\uff0c\u8fd9\u5c31\u662f\u67d3\u8272\u8d28\u7586\u57df\uff0c\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/li>\n<\/ol>\n

    <\/p>\n

      \n
    1. \u6574\u4e2a\u57fa\u56e0\u7ec4\u88ab\u5206\u5272\u4e3a\u4e24\u4e2a\u7a7a\u95f4\u533a\u5ba4\uff0c\u5206\u522b\u6807\u8bb0\u4e3aA\uff0cB\u67d3\u8272\u8d28\u533a\u5ba4\uff0c\u5f80\u5f80\u533a\u5ba4\u5185\u4e92\u4f5c\u9891\u7e41\uff0c\u800c\u533a\u5ba4\u95f4\u4e92\u4f5c\u8f83\u5c11\u3002\u5728\u751f\u7269\u4fe1\u606f\u5206\u6790\u4e2d\uff0c\u901a\u5e38\u901a\u8fc7\u8ba1\u7b97\u67d3\u8272\u4f53\u5185\u90e8\u4e92\u4f5c\u7684\u76f8\u5173\u6027\u6765\u533a\u5206\u4e24\u79cd\u4e0d\u540c\u7684\u533a\u5ba4\u3002\u5176\u4e2dA\u533a\u5ba4\u662f\u5f00\u653e\u7684\u67d3\u8272\u8d28\uff0c\u8868\u8fbe\u6d3b\u8dc3\uff0c\u57fa\u56e0\u4e30\u5bcc\uff0c\u5177\u6709\u8f83\u9ad8\u7684CG\u542b\u91cf\uff0c\u5305\u542b\u7528\u4e8e\u4e3b\u52a8\u8f6c\u5f55\u7684\u7ec4\u86cb\u767d\u6807\u8bb0\uff0c\u901a\u5e38\u4f4d\u4e8e\u7ec6\u80de\u6838\u5185\u90e8\uff1b\u800cB\u533a\u5ba4\u662f\u5173\u95ed\u7684\u67d3\u8272\u8d28\uff0c\u8868\u8fbe\u4e0d\u6d3b\u8dc3\uff0c\u57fa\u56e0\u7f3a\u4e4f\uff0c\u7ed3\u6784\u7d27\u51d1\uff0c\u542b\u6709\u57fa\u56e0\u6c89\u9ed8\u7684\u7ec4\u86cb\u767d\u6807\u5fd7\u7269\uff0c\u4f4d\u4e8e\u7ec6\u80de\u6838\u7684\u5916\u56f4\u3002AB\u533a\u5ba4\u793a\u610f\u56fe\u5982\u4e0b\u6240\u793a\uff1a<\/li>\n<\/ol>\n

      <\/p>\n

        \n
      1. \u5728\u67d3\u8272\u8d28\u533a\u5ba4\u4e2d\uff0c\u8fd8\u5b58\u5728\u4e92\u76f8\u4f5c\u7528\u76f8\u5bf9\u9891\u7e41\u7684\u57fa\u56e0\u533a\u57df\uff0c\u88ab\u79f0\u4e3a\u62d3\u6251\u7ed3\u6784\u57df\uff08TAD\uff09\u3002\u8fd9\u4e9b\u533a\u57df\u5728\u4e0d\u540c\u7684\u54fa\u4e73\u52a8\u7269\u7684\u4e0d\u540c\u7ec6\u80de\u4e2d\u90fd\u5f88\u4fdd\u5b88\uff0c\u5e76\u4e14\u9ad8\u5ea6\u5bcc\u96c6CTCF\u548c\u7c98\u9644\u86cb\u767d\u3002TAD\u7ed3\u6784\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/li>\n<\/ol>\n

        <\/p>\n

        \u4e0a\u9762\u5e26\u5927\u5bb6\u4e86\u89e3\u4e86\u90e8\u5206\u4e09\u7ef4\u57fa\u56e0\u7ec4\u7684\u77e5\u8bc6\uff0c\u4e0b\u9762\u5c0f\u679c\u5e26\u5927\u5bb6\u8fdb\u884c\u4e09\u7ef4\u57fa\u56e0\u7ec4\u7684AB\u533a\u5ba4\u5206\u6790\uff0c\u53d1\u8f66\u54af<\/p>\n

        \u76ee\u524d\u6bd4\u8f83\u6d41\u884c\u7684\u8ba1\u7b97AB\u533a\u5ba4\u7684\u8f6f\u4ef6\u4e3b\u8981\u6709\u4e00\u4e0b\u4e09\u79cd\uff1a<\/p>\n

          \n
        1. juicer: \u7b2c\u4e00\u7bc7HiC\u6587\u7ae0\u5b9e\u9a8c\u5ba4\u63d0\u4f9b\u7684\u5de5\u5177\uff0c\u8ba1\u7b97\u591a\u4e2a\u5206\u8fa8\u7387\u6bcf\u4e2abin\u7684PC1\u503c\uff0c\u4f46\u662f\u8f93\u51fa\u53ea\u6709\u4e00\u5217\uff0c\u4e0d\u662fbedgraph\u6587\u4ef6\uff0c\u4e0d\u592a\u4eba\u6027\u5316\uff1b\u540c\u65f6\u4e0d\u80fd\u5224\u65adAB\u533a\u5ba4\uff0c\u9700\u8981\u81ea\u5df1\u624b\u52a8\u6821\u6b63\u3002<\/li>\n
        2. homer: NGS\u5206\u6790\u5957\u4ef6\uff0c\u4e5f\u6709HiC\u5206\u6790\u6d41\u7a0b\uff0c\u53ef\u4ee5\u901a\u8fc7TSS\u6216\u8005ATAC\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u5224\u65adAB\u533a\u5ba4\uff0c\u4e5f\u53ef\u4ee5\u8f93\u51fabedgraph\u6587\u4ef6\u548c\u77e9\u9635\u6587\u4ef6\u3002<\/li>\n
        3. cworld: \u4e00\u79cd\u57fa\u4e8ePerl\u7684HiC\u5206\u6790\u5de5\u5177\uff0c\u53ef\u4ee5\u8ba1\u7b97AB\u533a\u5ba4\u548cTAD\u7b49\u7ed3\u6784\u3002<\/li>\n<\/ol>\n

          \u4e0a\u8ff0\u4e09\u4e2a\u8f6f\u4ef6\u7684\u4f18\u7f3a\u70b9\u5982\u4e0b\uff1a<\/p>\n

            \n
          1. juicer: \u4f18\u70b9\u662f\u7b2c\u4e00\u7bc7HiC\u6587\u7ae0\u5b9e\u9a8c\u5ba4\u63d0\u4f9b\u7684\u5de5\u5177\uff0c\u6709\u6743\u5a01\u6027\u548c\u53ef\u9760\u6027\uff0c\u53ef\u4ee5\u8ba1\u7b97\u591a\u4e2a\u5206\u8fa8\u7387\u6bcf\u4e2abin\u7684PC1\u503c\uff1b\u7f3a\u70b9\u662f\u8f93\u51fa\u53ea\u6709\u4e00\u5217\uff0c\u4e0d\u662fbedgraph\u6587\u4ef6\uff0c\u4e0d\u592a\u4eba\u6027\u5316\uff0c\u540c\u65f6\u4e0d\u80fd\u5224\u65adAB\u533a\u5ba4\uff0c\u9700\u8981\u81ea\u5df1\u624b\u52a8\u6821\u6b63\u3002<\/li>\n
          2. homer: \u4f18\u70b9\u662fNGS\u5206\u6790\u5957\u4ef6\uff0c\u4e5f\u6709HiC\u5206\u6790\u6d41\u7a0b\uff0c\u53ef\u4ee5\u901a\u8fc7TSS\u6216\u8005ATAC\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u5224\u65adAB\u533a\u5ba4\uff0c\u4e5f\u53ef\u4ee5\u8f93\u51fabedgraph\u6587\u4ef6\u548c\u77e9\u9635\u6587\u4ef6\uff1b\u7f3a\u70b9\u662f\u5b89\u88c5\u914d\u7f6e\u6bd4\u8f83\u590d\u6742\uff0c\u9700\u8981\u4e0b\u8f7d\u6216\u8005\u6784\u5efa\u57fa\u56e0\u7ec4\u4fe1\u606f\u3002<\/li>\n
          3. cworld: \u4f18\u70b9\u662f\u4e00\u79cd\u57fa\u4e8ePerl\u7684HiC\u5206\u6790\u5de5\u5177\uff0c\u53ef\u4ee5\u8ba1\u7b97AB\u533a\u5ba4\u548cTAD\u7b49\u7ed3\u6784\uff0c\u4e5f\u53ef\u4ee5\u8f93\u51fa\u77e9\u9635\u6587\u4ef6\uff1b\u7f3a\u70b9\u662f\u6587\u6863\u4e0d\u592a\u5b8c\u5584\uff0c\u4f7f\u7528\u4e0d\u592a\u65b9\u4fbf\u3002<\/li>\n<\/ol>\n

            \u5927\u5bb6\u4e86\u89e3\u4e86\u8fd9\u4e09\u4e2a\u8f6f\u4ef6\u7684\u533a\u522b\u4e4b\u540e\uff0c\u662f\u4e0d\u662f\u611f\u89c9homer\u8f6f\u4ef6\u66f4\u5168\u9762\u5462\uff0c\u53cd\u6b63\u5c0f\u679c\u9009\u62e9\u7684\u662fHiC-Pro+homer\u6765\u8fdb\u884cAB\u533a\u5ba4\u8ba1\u7b97\u7684\u3002<\/p>\n

            \u9996\u5148\u9700\u8981\u7528\u5230\u7684\u662fHiC-Pro\u8f6f\u4ef6\u751f\u6210\u7684.allValidPairs\u6587\u4ef6\uff0c\u6ca1\u6709\u4f7f\u7528\u8fc7HiC-Pro\u8f6f\u4ef6\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u53bb\u770b\u4ee5\u524d\u5c0f\u679c\u7684\u6587\u7ae0\u55f7\u3002<\/p>\n

            \u4e0b\u9762\u662f\u683c\u5f0f\u7684\u8f6c\u6362\uff0c\u4fee\u6539.allValidPairs\u6587\u4ef6\u683c\u5f0f\uff0c\u5c06HiC-Pro\u8f93\u51fa\u6587\u4ef6\uff0c\u8f6c\u6362\u6210homer\u683c\u5f0f\uff1a<\/p>\n

            cat $test.allValidPairs | awk ‘BEGIN{FS=OFS=”\\t”}{print NR,$2,$3,$4,$5,$6,$7}’ > test.homer<\/p>\n

            \u4e0b\u9762\u662fhomer\u8f6f\u4ef6\u7684\u5b89\u88c5\uff1a<\/p>\n

            HOMER\u7684\u5b89\u88c5\u53ef\u4ee5\u4f7f\u7528conda\u6765\u5b8c\u6210\uff1a<\/p>\n

            conda install -c bioconda homer<\/p>\n

            \u4e0b\u9762\u9700\u8981configureHomer.pl\u5b8c\u6210Homer\u8f6f\u4ef6\u7684\u914d\u7f6e\uff1a<\/p>\n

              \n
            1. \u5148\u4e0b\u8f7dconfigureHomer.pl\uff1a<\/li>\n<\/ol>\n

              wget\u00a0http:\/\/homer.ucsd.edu\/homer\/configureHomer.pl<\/p>\n

                \n
              1. \u4f7f\u7528configureHomer.pl\u914d\u7f6eHomer\uff08\u5c0f\u4f19\u4f34\u4eec\u6ce8\u610f\u6587\u4ef6\u8def\u5f84\u95ee\u9898\u55f7\uff09<\/li>\n<\/ol>\n

                perl\u00a0configureHomer.pl \u00a0[options]<\/p>\n

                \u5927\u5bb6\u53ef\u4ee5\u4f7f\u7528configureHomer.pl\u6765\u914d\u7f6eHomer\uff0c\u4f8b\u5982\u4e0b\u8f7d\u4eba\u7c7b\uff0c\u5c0f\u9f20\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u7b49<\/p>\n

                \u4e07\u4e8b\u5177\u5907\uff0c\u53ea\u6b20\u4e1c\u98ce\u3002\u4e0b\u9762\u5c0f\u679c\u5f00\u59cb\u5206\u6790\uff0c\u5c0f\u679c\u7684\u4ee3\u7801\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n

                ## \u7b2c\u4e00\u6b65 makeTagDir<\/p>\n

                # -format\u6307\u5b9a\u683c\u5f0f\uff0ctest.homer\u4e3a\u8f93\u5165\u7684homer\u683c\u5f0f\u6587\u4ef6<\/p>\n

                makeTagDirectory test -format HiCsummary test.homer<\/p>\n

                ## step 2 : calculate PC1 value<\/p>\n

                # test-500k\u4e3a\u751f\u6210\u6587\u4ef6\u524d\u7f00\uff0c-res\u662f\u4ee5bp\u4e3a\u5355\u4f4d\u7684\u5206\u8fa8\u7387\uff0c-genome\u4e3a\u53c2\u8003\u57fa\u56e0\u7ec4<\/p>\n

                runHiCpca.pl test-500k test -cpu 32 -res 500000 -genome hg38.fasta -pc 1<\/p>\n

                \u7ed3\u679c\u4f1a\u751f\u6210\u4e24\u4e2a\u6587\u4ef6\uff0c\u5206\u522b\u662fbedGraph\u6587\u4ef6txt\u6587\u4ef6<\/p>\n

                \u5c0f\u679c\u7684bedGraph\u6587\u4ef6\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n

                <\/p>\n

                Txt\u6587\u4ef6\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n

                <\/p>\n

                \u4e24\u4e2a\u6587\u4ef6\u7684\u5185\u5bb9\u5927\u81f4\u76f8\u540c\uff0c\u53ea\u662f\u683c\u5f0f\u4e0d\u540c\uff0cbedGraph\u6587\u4ef6\u53ef\u4f7f\u7528IGV\u8f6f\u4ef6\u8fdb\u884c\u53ef\u89c6\u5316\uff0c\u5c0f\u679c\u7684\u53ef\u89c6\u5316\u7ed3\u679c\u5982\u4e0b\u56fe\uff1a<\/p>\n

                <\/p>\n

                \u4ee511\u67d3\u8272\u4f53\u4e3a\u4f8b\uff0c\u5927\u5bb6\u53ef\u4ee5\u6e05\u695a\u7684\u770b\u5230\u67d3\u8272\u4f53\u88ab\u5206\u4e3aAB\u4e24\u4e2a\u533a\u5ba4\uff08\u4ee5PC1\u503c\u5212\u5206\uff09<\/p>\n

                \u4eca\u5929\u7684\u5173\u4e8e\u4e09\u4f4d\u57fa\u56e0\u7ec4AB\u533a\u5ba4\u7684\u8ba1\u7b97\u5b66\u4e60\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u627e\u5c0f\u679c\u8ba8\u8bba\uff0c\u6709\u611f\u89c9\u751f\u4fe1\u5206\u6790\u590d\u6742\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528\u6211\u4eec\u7684\u751f\u4fe1\u5c0f\u5de5\u5177\u54e6\uff0c\u94fe\u63a5\u5728\u8fd9\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/a>\uff0c\u6211\u4eec\u660e\u5929\u89c1\u54af~<\/p>\n","protected":false},"excerpt":{"rendered":"

                \u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u53c8\u8ddf\u5927\u5bb6\u89c1\u9762\u5566\uff01\u8fd9\u6b21\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u4e09\u7ef4\u57fa\u56e0\u7ec4\u7684AB\u533a\u5ba4\u5206\u6790\u7684\u5185\u5bb9 \u4ee5\u9632\u5c0f\u4f19\u4f34\u4eec\u8ddf\u4e0d\u4e0a\u5c0f\u679c\u7684\u8282\u594f\uff0c\u5c0f […]<\/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\/24275"}],"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=24275"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24275\/revisions"}],"predecessor-version":[{"id":24282,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24275\/revisions\/24282"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24275"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24275"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24275"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}