{"id":23918,"date":"2024-01-09T17:37:52","date_gmt":"2024-01-09T09:37:52","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23918"},"modified":"2024-01-09T17:37:54","modified_gmt":"2024-01-09T09:37:54","slug":"peak%e6%b3%a8%e9%87%8a%ef%bc%9fhomer%e6%9d%a5%e5%b8%ae%e4%bd%a0%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23918","title":{"rendered":"Peak\u6ce8\u91ca\uff1fHOMER\u6765\u5e2e\u4f60\uff01"},"content":{"rendered":"

\u4e0d\u77e5\u9053\u5c0f\u4f19\u4f34\u4eec\u662f\u5426\u7406\u89e3Peak\u7684\u542b\u4e49\u5462? \u8fd9\u91cc\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u7406\u89e3\u4e00\u4e0bATAC-seq\u4e2d\u7684peak<\/p>\n

\u9996\u5148\u5148\u4ecb\u7ecd\u4e00\u4e0bATAC-seq\uff1aATAC-seq\u662f\u4e00\u79cd\u6d4b\u91cf\u67d3\u8272\u8d28\u53ef\u53ca\u6027\u7684\u6280\u672f\uff0c\u5229\u7528\u8f6c\u5ea7\u9176Tn5\u5728\u5f00\u653e\u67d3\u8272\u8d28\u533a\u57df\u5207\u5272DNA\u5e76\u63d2\u5165\u6d4b\u5e8f\u63a5\u5934\uff0c\u4ece\u800c\u53ef\u4ee5\u901a\u8fc7\u9ad8\u901a\u91cf\u6d4b\u5e8f\u68c0\u6d4b\u5230\u54ea\u4e9b\u533a\u57df\u662f\u67d3\u8272\u8d28\u5f00\u653e\u7684\u3002\u90a3\u4e48ATAC-seq\u4e2d\u7684peak\u662f\u6307\u5728\u67d0\u4e00\u4f4d\u7f6e\u6216\u533a\u57df\uff0c\u6d4b\u5e8f\u4fe1\u53f7\u8fbe\u5230\u6700\u5927\u503c\u7684\u73b0\u8c61\uff0c\u901a\u5e38\u53cd\u6620\u4e86\u67d0\u79cd\u57fa\u56e0\u8c03\u63a7\u5143\u4ef6\uff08\u5982\u542f\u52a8\u5b50\u3001\u589e\u5f3a\u5b50\u7b49\uff09\u6216\u8f6c\u5f55\u56e0\u5b50\u7ed3\u5408\u4f4d\u70b9\u7684\u5b58\u5728\u3002ATAC-seq\u7684peak\u5206\u6790\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u53d1\u73b0\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u6216\u72b6\u6001\u4e0b\uff0c\u67d3\u8272\u8d28\u53ef\u53ca\u6027\u7684\u53d8\u5316\uff0c\u4ee5\u53ca\u4e0e\u4e4b\u76f8\u5173\u7684\u8f6c\u5f55\u8c03\u63a7\u673a\u5236\u3002<\/p>\n

\u4f8b\u5982\u4e0b\u56fe\uff1a<\/p>\n

<\/p>\n

\u56fe\u4e2d\u7684\u4e00\u4e2a\u4e2a\u7a81\u8d77\u7684\u5c0f\u5c71\u5cf0\u5c31\u662f\u6211\u4eec\u4eca\u5929\u7684\u4e3b\u89d2peak\u4e86\u3002<\/p>\n

\u90a3peak\u600e\u4e48\u5f97\u5230\u5462\uff1f\u53c8\u4e3a\u4ec0\u4e48\u8981\u53bb\u6ce8\u91ca\u5462\uff1f<\/p>\n

\u5c0f\u4f19\u4f34\u4eec\u662f\u4e0d\u662f\u6709\u70b9\u6655\u5462\uff1f\u54c8\u54c8\u54c8\u4e0d\u8981\u7740\u6025\uff0c\u4e14\u542c\u5c0f\u679c\u7ec6\u7ec6\u9053\u6765<\/p>\n

\u9996\u5148\u6211\u4eec\u7684ATAC-seq\u7684\u6d4b\u5e8f\u6570\u636erow data\u7ecf\u8fc7\u6e05\u7406\u4e4b\u540e\u5f97\u5230clean data\uff0c\u7136\u540e\u5bf9clean data\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u4e4b\u540e\u5f97\u5230bam\u6587\u4ef6\uff0c\u7ecf\u8fc7\u6392\u5e8f\uff0c\u6807\u8bb0\u5355\u7aef\u6bd4\u5bf9\uff08\u53cc\u7aef\u6d4b\u5e8f\uff09\uff0c\u53bb\u9664PCR\u91cd\u590d\u7b49\u8fc7\u7a0b\u5c31\u4f1a\u5f97\u5230\u6700\u7ec8\u7684final bam\u6587\u4ef6\uff0c\u7136\u540e\u5c31\u53ef\u4ee5\u91c7\u7528MACS2 \u8f6f\u4ef6\u6765\u5f97\u5230peak\u5566<\/p>\n

\u90a3\u4e48\u4e3a\u4ec0\u4e48\u8981\u5bf9peak\u8fdb\u884c\u6ce8\u91ca\u5462\uff1fPeak\u7684\u6ce8\u91ca\u662f\u5c06peak\u4e0e\u57fa\u56e0\u7ec4\u4e0a\u7684\u5df2\u77e5\u5143\u4ef6\uff08\u5982\u57fa\u56e0\u3001\u8f6c\u5f55\u8d77\u59cb\u4f4d\u70b9\u3001\u542f\u52a8\u5b50\u3001\u589e\u5f3a\u5b50\u7b49\uff09\u8fdb\u884c\u6bd4\u8f83\u548c\u5bf9\u5e94\uff0c\u4ece\u800c\u63a8\u65adpeak\u7684\u529f\u80fd\u548c\u4f5c\u7528\u5bf9\u8c61123\u3002Peak\u7684\u6ce8\u91ca\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u7406\u89e3peak\u5728\u57fa\u56e0\u8c03\u63a7\u7f51\u7edc\u4e2d\u7684\u89d2\u8272\uff0c\u53d1\u73b0\u4e0epeak\u76f8\u5173\u7684\u57fa\u56e0\u548c\u8f6c\u5f55\u56e0\u5b50\uff0c\u4ee5\u53ca\u63a2\u7d22\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u6216\u72b6\u6001\u4e0b\uff0cpeak\u7684\u5dee\u5f02\u548c\u53d8\u5316\u3002\u6362\u53e5\u8bdd\u8bf4\u662f\u56e0\u4e3a\u5355\u7eaf\u7684peak\u53ea\u662f\u4e00\u4e9b\u51b0\u51b7\u7684\u6570\u636e\uff0c\u53ea\u6709\u901a\u8fc7\u6ce8\u91ca\uff0c\u624d\u80fd\u5c06peak\u5339\u914d\u5230\u4e00\u4e9b\u57fa\u56e0\u5143\u4ef6\u4e0a\u3002<\/p>\n

\u4e0b\u9762\u5c0f\u679c\u8bb2\u4e00\u4e0b\u600e\u4e48\u7528HOMER\u8f6f\u4ef6\u53bb\u6ce8\u91capeak<\/p>\n

HOMER\u8f6f\u4ef6\u662f\u4e00\u79cd\u7528\u4e8e\u5206\u6790\u548c\u6ce8\u91ca\u57fa\u56e0\u7ec4\u4e0a\u7684peak\u7684\u5de5\u5177\uff0c\u4e3b\u8981\u7528\u4e8eChIP-seq\uff0cATAC-seq\u6570\u636e\u7684\u5904\u7406\u3002HOMER\u8f6f\u4ef6\u53ef\u4ee5\u63d0\u4f9b\u4ee5\u4e0b\u529f\u80fd\uff1a<\/p>\n

    \n
  1. \u5bfb\u627e\u548c\u6ce8\u91ca\u4e0e\u8f6c\u5f55\u56e0\u5b50\u6216\u7ec4\u86cb\u767d\u4fee\u9970\u76f8\u5173\u7684peak<\/li>\n
  2. \u6bd4\u8f83\u4e0d\u540c\u6837\u672c\u6216\u6761\u4ef6\u4e0b\u7684peak\u5dee\u5f02<\/li>\n
  3. \u8bc6\u522b\u548c\u5206\u6790\u8f6c\u5f55\u56e0\u5b50\u7ed3\u5408\u4f4d\u70b9\u7684motif<\/li>\n
  4. \u8bc4\u4f30peak\u5728\u57fa\u56e0\u8868\u8fbe\u8c03\u63a7\u4e2d\u7684\u4f5c\u7528<\/li>\n
  5. \u53ef\u89c6\u5316peak\u5728\u57fa\u56e0\u7ec4\u4e0a\u7684\u5206\u5e03\u548c\u7279\u5f81<\/li>\n<\/ol>\n

    \u9996\u5148\u8f6f\u4ef6\u7684\u5b89\u88c5\uff1a\u6211\u4eec\u679c\u65ad\u9009\u62e9conda\uff1a<\/p>\n

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

    \u5b89\u88c5\u5b8cHOMER\u4e4b\u540e\u4f7f\u7528configureHomer.pl\u5b8c\u6210HOMER\u8f6f\u4ef6\u7684\u914d\u7f6e<\/p>\n

      \n
    1. # \u4e0b\u8f7d\u914d\u7f6e\u6587\u4ef6<\/li>\n
    2. wget http:\/\/homer.salk.edu\/homer\/configureHomer.pl<\/li>\n
    3. # \u4f7f\u7528\u914d\u7f6e\u6587\u4ef6\u8fdb\u884c\u8f6f\u4ef6\u914d\u7f6e<\/li>\n
    4. perl configureHomer.pl -install<\/li>\n<\/ol>\n

      \u5982\u679c\u662f\u4eba\u7c7b\u548c\u5c0f\u9f20\u7b49\u7684\u6570\u636e\u5c31\u76f4\u63a5\u53ef\u4ee5\u7528configureHomer.pl\u6765\u4e0b\u8f7d\u76f8\u5e94\u7684\u53c2\u8003\u57fa\u56e0\u7ec4<\/p>\n

      \u4ee5\u4eba\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u4e3a\u4f8b\uff1a<\/p>\n

        \n
      1. perl configureHomer.pl -install hg19<\/li>\n<\/ol>\n

        \u5982\u679c\u662f\u81ea\u5b9a\u4e49HOMER\u6570\u636e\u7684\u8bdd\u9700\u8981\u53c2\u8003\u57fa\u56e0\u7ec4\u7684fasta\u6587\u4ef6\u548cgtf\u6587\u4ef6\uff0c\u4f7f\u7528loadGenome.pl\u547d\u4ee4\u6765\u81ea\u5b9a\u4e49HOMER\uff08\u9700\u8981HOMER\u7248\u672c4.4\u4ee5\u4e0a\uff09<\/p>\n

          \n
        1. loadGenome.pl -gtf test.gtf -name test -fasta test_assembly.fa -org null<\/li>\n<\/ol>\n

          \u63a5\u4e0b\u6765\u5c31\u662fpeak\u7684\u6ce8\u91ca\u5566\uff0cpeak\u7684\u6ce8\u91ca\u9700\u8981\u7528\u5230annotatePeaks.pl\u00a0\u547d\u4ee4\uff0c\u8f93\u5165\u6587\u4ef6\u53ef\u4ee5\u662fMACS2\u8f6f\u4ef6callpeak\u7684bed\u6587\u4ef6(\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528)\u6216\u8005\u662fHOMER\u8f6f\u4ef6\u6307\u5b9a\u7684peak\u6587\u4ef6\u683c\u5f0f\u3002peak\u6587\u4ef6\u683c\u5f0f\uff1a\u4f7f\u7528Tab\u5206\u9694\uff0c\u5171\u4e94\u5217\uff0c\u5206\u522b\u662f peak ID , chr , start , end ,strand<\/p>\n

          annotatePeaks.pl\u00a0<Homer<\/strong>\u00a0Peak\/Positions\u00a0file>\u00a0<genome<\/strong>>\u00a0\u00a01> peak.anno.xls\u00a0 2> anno.log<\/p>\n

          \u5c0f\u679c\u7684\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

          annotatePeaks.pl test.bed Bomo 1> peak.anno.xlsx 2> anno.log<\/p>\n

          \u7ed3\u679c\u4f1a\u751f\u6210\u4e00\u4e2axlsx\u6587\u4ef6\uff0c\u91cc\u9762\u662f\u6ce8\u91ca\u7684\u7ed3\u679c\u4fe1\u606f<\/p>\n

          <\/p>\n

          \u4eca\u5929HOMER\u6ce8\u91capeak\u7684\u5b66\u4e60\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u627e\u5c0f\u679c\u8ba8\u8bba\u54e6\uff0c\u6211\u4eec\u660e\u5929\u89c1\u54af~<\/p>\n","protected":false},"excerpt":{"rendered":"

          \u4e0d\u77e5\u9053\u5c0f\u4f19\u4f34\u4eec\u662f\u5426\u7406\u89e3Peak\u7684\u542b\u4e49\u5462? \u8fd9\u91cc\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u7406\u89e3\u4e00\u4e0bATAC-seq\u4e2d\u7684peak \u9996\u5148\u5148\u4ecb\u7ecd\u4e00\u4e0b […]<\/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\/23918"}],"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=23918"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23918\/revisions"}],"predecessor-version":[{"id":23921,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23918\/revisions\/23921"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23918"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23918"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23918"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}