{"id":23855,"date":"2024-01-09T17:27:48","date_gmt":"2024-01-09T09:27:48","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23855"},"modified":"2024-01-09T17:27:49","modified_gmt":"2024-01-09T09:27:49","slug":"%e6%83%8a%e6%8e%89%e4%b8%8b%e5%b7%b4%ef%bc%81%e4%bd%a0%e4%b8%8d%e7%9f%a5%e9%81%93%e7%9a%84atac-seq%e9%87%8d%e5%a4%8d%e6%a0%b7%e6%9c%ac%e5%a4%84%e7%90%86%e6%96%b9%e5%bc%8f","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23855","title":{"rendered":"\u60ca\u6389\u4e0b\u5df4\uff01\u4f60\u4e0d\u77e5\u9053\u7684ATAC-seq\u91cd\u590d\u6837\u672c\u5904\u7406\u65b9\u5f0f"},"content":{"rendered":"

\u5c0f\u679c\u8bfe\u5802\u968f\u673a\u63d0\u95ee\uff1a\u5c0f\u4f19\u4f34\u4eec\u77e5\u9053\u91cd\u590d\u6837\u672c\u5e94\u8be5\u600e\u4e48\u6837\u5904\u7406\u5417\uff1f<\/p>\n

\u4e0b\u9762\u662f\u4e00\u4e9b\u57fa\u7840\u77e5\u8bc6\uff1a<\/p>\n

\u91cd\u590d\u6837\u672c\u7684\u5904\u7406\u65b9\u5f0f\u662f\u6307\u5728\u6570\u636e\u5206\u6790\u4e2d\uff0c\u5982\u4f55\u5904\u7406\u540c\u4e00\u7ec4\u6216\u540c\u4e00\u6837\u672c\u7684\u591a\u6b21\u6d4b\u91cf\u6216\u5206\u6790\u7ed3\u679c\u3002\u91cd\u590d\u6837\u672c\u7684\u5904\u7406\u65b9\u5f0f\u53ef\u80fd\u56e0\u4e3a\u4e0d\u540c\u7684\u7814\u7a76\u76ee\u7684\u548c\u6570\u636e\u7279\u5f81\u800c\u6709\u6240\u4e0d\u540c\uff0c\u4f46\u4e00\u822c\u53ef\u4ee5\u5206\u4e3a\u4ee5\u4e0b\u51e0\u79cd\uff1a<\/p>\n

    \n
  1. \u6837\u672c\u91cd\u590d\u6027\u68c0\u9a8c\uff1a\u901a\u8fc7\u8ba1\u7b97\u6837\u672c\u95f4\u7684\u76f8\u5173\u7cfb\u6570\u3001\u7ed8\u5236\u6837\u672c\u805a\u7c7b\u56fe\u6216\u4e3b\u6210\u5206\u5206\u6790\u56fe\u7b49\u65b9\u6cd5\uff0c\u8bc4\u4f30\u7ec4\u5185\u6837\u672c\u7684\u91cd\u590d\u6027\u662f\u5426\u826f\u597d\uff0c\u662f\u5426\u6709\u79bb\u7fa4\u6837\u672c\u9700\u8981\u5254\u9664\u3002<\/li>\n
  2. \u6837\u672c\u8fc7\u62bd\u6837\u6216\u6b20\u62bd\u6837\uff1a\u5f53\u6570\u636e\u5b58\u5728\u4e0d\u5747\u8861\u95ee\u9898\u65f6\uff0c\u53ef\u4ee5\u901a\u8fc7\u589e\u52a0\u5c11\u6570\u7c7b\u6837\u672c\u6216\u51cf\u5c11\u591a\u6570\u7c7b\u6837\u672c\u7684\u65b9\u6cd5\uff0c\u4f7f\u6570\u636e\u66f4\u52a0\u5747\u8861\u3002<\/li>\n
  3. \u6837\u672c\u6743\u91cd\u8c03\u6574\uff1a\u5f53\u6570\u636e\u5b58\u5728\u4e0d\u5747\u8861\u95ee\u9898\u65f6\uff0c\u4e5f\u53ef\u4ee5\u901a\u8fc7\u7ed9\u5c11\u6570\u7c7b\u6837\u672c\u8d4b\u4e88\u66f4\u9ad8\u7684\u6743\u91cd\u6216\u7ed9\u591a\u6570\u7c7b\u6837\u672c\u8d4b\u4e88\u66f4\u4f4e\u7684\u6743\u91cd\u7684\u65b9\u6cd5\uff0c\u4f7f\u6570\u636e\u66f4\u52a0\u5747\u8861\u3002<\/li>\n
  4. \u6837\u672c\u6df7\u5408\u6216\u5e73\u5747\uff1a\u5f53\u6570\u636e\u5b58\u5728\u8f83\u5927\u7684\u4e2a\u4f53\u5dee\u5f02\u6216\u80cc\u666f\u6ce2\u52a8\u65f6\uff0c\u53ef\u4ee5\u901a\u8fc7\u5c06\u591a\u4e2a\u6837\u672c\u6df7\u5408\u4f5c\u4e3a\u4e00\u4e2a\u751f\u7269\u5b66\u91cd\u590d\u6216\u5bf9\u591a\u4e2a\u6280\u672f\u91cd\u590d\u53d6\u5e73\u5747\u503c\u7684\u65b9\u6cd5\uff0c\u964d\u4f4e\u6570\u636e\u7684\u566a\u58f0\u3002<\/li>\n<\/ol>\n

    \u4e0a\u9762\u662f\u4e00\u4e9b\u5e38\u89c1\u7684\u91cd\u590d\u6837\u672c\u7684\u5904\u7406\u65b9\u5f0f\uff0c\u5177\u4f53\u5e94\u7528\u65f6\u9700\u8981\u6839\u636e\u5b9e\u9a8c\u8bbe\u8ba1\u548c\u6570\u636e\u7279\u70b9\u8fdb\u884c\u9009\u62e9\u548c\u4f18\u5316\u3002<\/p>\n

    \u5c0f\u679c\u6700\u8fd1\u6c89\u8ff7ATAC-seq\uff0c\u90a3\u5c31\u4ee5ATAC-seq\u5f53\u4f8b\u5b50\u6765\u6559\u5927\u5bb6\u91cd\u590d\u6837\u672c\u7684\u5904\u7406\u65b9\u5f0f\u5427<\/p>\n

    \u9488\u5bf9ATAC-seq\u6570\u636e\uff0c\u8981\u6c42\u5fc5\u987b\u67092\u6b21\u6216\u66f4\u591a\u6b21\u751f\u7269\u5b66\u91cd\u590d\uff08\u5341\u5206\u73cd\u8d35\u6216\u8005\u7a00\u6709\u6837\u672c\u9664\u5916\uff0c\u4f46\u5fc5\u987b\u505a\u81f3\u5c112\u6b21\u6280\u672f\u91cd\u590d\uff09\u3002\u7406\u8bba\u4e0a\u91cd\u590d\u6837\u672c\u7684peaks\u5e94\u8be5\u6709\u9ad8\u5ea6\u7684\u4e00\u81f4\u6027\uff0c\u5b9e\u9645\u60c5\u51b5\u5e76\u4e0d\u5b8c\u5168\u4e0e\u9884\u671f\u4e00\u81f4\u3002\u5982\u4f55\u8bc4\u4ef7\u91cd\u590d\u6837\u672c\u7684\u91cd\u590d\u6027\u7684\u597d\u574f\uff1f\u5982\u4f55\u5f97\u5230\u4e00\u81f4\u6027\u7684peaks?<\/p>\n

    \u4e0a\u9762\u7684\u51e0\u4e2a\u95ee\u9898\u662f\u4e0d\u662f\u53c8\u7ed9\u5c0f\u4f19\u4f34\u4eec\u6574\u6655\u4e86\u5462\uff1f<\/p>\n

    \u4e0b\u9762\u5c0f\u679c\u6559\u5927\u5bb6\u4f7f\u7528IDR\u6765\u5904\u7406ATAC-seq\u4e2d\u7684\u91cd\u590d\u6837\u672c<\/p>\n

    \u9996\u5148\u662fIDR\u8f6f\u4ef6\u7684\u4e0b\u8f7d<\/p>\n

    IDR\u7684\u5b89\u88c5\u5341\u5206\u7b80\u5355\uff0c\u5b83\u7684\u5b89\u88c5\u65b9\u6cd5\u6709\u591a\u79cd\uff0c\u6700\u7b80\u5355\u7684\u4e00\u79cd\u662f\u4f7f\u7528 conda \u547d\u4ee4\uff1a<\/p>\n

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

    \u8fd9\u6837\u53ef\u4ee5\u81ea\u52a8\u5b89\u88c5 idr\u53ca\u5176\u6240\u6709\u7684 python \u4f9d\u8d56\u9879<\/p>\n

    \u53e6\u4e00\u79cd\u65b9\u6cd5\u662f\u4f7f\u7528 pip \u547d\u4ee4\uff1a<\/p>\n

    pip install idr<\/p>\n

    \u8fd9\u6837\u4e5f\u53ef\u4ee5\u81ea\u52a8\u5b89\u88c5 idr\u53ca\u5176\u6240\u6709\u7684 python \u4f9d\u8d56\u9879<\/p>\n

    \u4e0d\u8fc7\u8fd9\u91cc\u5c0f\u679c\u8981\u5efa\u8bae\u5c0f\u4f19\u4f34\u4eec\u4f7f\u7528IDR\u65f6\uff0c\u5728MACS2 callpeak\u7684\u65f6\u5019\u53c2\u6570\u4e0d\u8981\u8bbe\u7f6e\u592a\u4e25\u683c\u54e6\uff0c\u8fd9\u6837\u624d\u80fd\u9274\u5b9a\u51fa\u66f4\u591a\u7684peak\uff0c\u5e76\u4e14\u4f7f\u7528IDR\u9700\u8981\u5148\u5bf9MACS2\u7684\u7ed3\u679c\u6587\u4ef6narrowPeak\u6839\u636e-log10(p-value)\u8fdb\u884c\u6392\u5e8f<\/p>\n

    \u4e0b\u9762\u662f\u5c0f\u679c\u7684\u4ee3\u7801\uff1a<\/p>\n

    # \u53c2\u6570\u8bbe\u7f6e\u53ef\u4ee5\u9002\u5f53\u653e\u5bbd<\/p>\n

    macs2 callpeak -t test.final.bam -n sample –shift -100 –extsize 200 –nomodel -B –SPMR -g hs 2> sample.macs2.log<\/p>\n

    # \u5bf9peak \u6309\u7167 -log10(p-value) \u6392\u5e8f<\/p>\n

    sort -k8,8nr sample_peaks.narrowPeak > sample_peaks.sort.narrowPeak<\/p>\n

    \u4e0b\u9762\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528idr \u6765\u5904\u7406\u91cd\u590d\u6837\u672c<\/p>\n

    \u5c0f\u679c\u7684\u4ee3\u7801\u662f\u8fd9\u6837\u7684\uff1a<\/p>\n

    idr –samples Rep1_sorted_peaks.narrowPeak Rep2_sorted_peaks.narrowPeak \\<\/p>\n

    –input-file-type narrowPeak \\<\/p>\n

    –rank p.value \\<\/p>\n

    –output-file idr \\<\/p>\n

    –plot \\<\/p>\n

    –log-output-file sample.idr.log<\/p>\n

    \u4e0b\u9762\u662f\u4e00\u4e9b\u53c2\u6570\u7684\u89e3\u91ca\uff1a<\/p>\n

      \n
    1. –samples: \u8f93\u5165\u6587\u4ef6<\/li>\n
    2. –input-file-type\uff1a\u8f93\u5165\u6587\u4ef6\u683c\u5f0f<\/li>\n
    3. –rank p.value\uff1a\u4ee5p-value\u6392\u5e8f<\/li>\n
    4. –output-file: \u8f93\u51fa\u6587\u4ef6\u8def\u5f84<\/li>\n
    5. –plot\uff1a\u7ed8\u5236\u7ed3\u679c\u56fe<\/li>\n<\/ol>\n

      \u5c0f\u679c\u63d0\u9192\u5927\u5bb6\uff0cidr\u6bcf\u6b21\u53ea\u80fd\u4e00\u6b21\u5904\u7406\u4e24\u4e2a\u6837\u672c\u54e6<\/p>\n

      \u8fd9\u662f\u5c0f\u679c\u7684\u7ed3\u679c\u56fe\uff0c\u662f\u4e0d\u662f\u5f88\u76f4\u89c2\u5462<\/p>\n

      <\/p>\n

      \u4eca\u5929\u7684ATAC-seq\u4e2d\u91cd\u590d\u6837\u672c\u5904\u7406\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":"

      \u5c0f\u679c\u8bfe\u5802\u968f\u673a\u63d0\u95ee\uff1a\u5c0f\u4f19\u4f34\u4eec\u77e5\u9053\u91cd\u590d\u6837\u672c\u5e94\u8be5\u600e\u4e48\u6837\u5904\u7406\u5417\uff1f \u4e0b\u9762\u662f\u4e00\u4e9b\u57fa\u7840\u77e5\u8bc6\uff1a \u91cd\u590d\u6837\u672c\u7684\u5904\u7406\u65b9\u5f0f\u662f\u6307\u5728\u6570\u636e\u5206 […]<\/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\/23855"}],"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=23855"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23855\/revisions"}],"predecessor-version":[{"id":23864,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23855\/revisions\/23864"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23855"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23855"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23855"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}