{"id":1891,"date":"2025-07-27T14:39:33","date_gmt":"2025-07-27T06:39:33","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1891"},"modified":"2025-07-27T18:48:02","modified_gmt":"2025-07-27T10:48:02","slug":"%e6%b5%85%e8%b0%88%e4%b8%80%e4%b8%8b%e7%9b%ae%e5%89%8d%e5%87%a0%e6%ac%be%e5%b8%b8%e7%94%a8%e7%9a%84%e6%9f%93%e8%89%b2%e4%bd%93%e6%8c%82%e8%bd%bd%e8%bd%af%e4%bb%b6","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/07\/27\/%e6%b5%85%e8%b0%88%e4%b8%80%e4%b8%8b%e7%9b%ae%e5%89%8d%e5%87%a0%e6%ac%be%e5%b8%b8%e7%94%a8%e7%9a%84%e6%9f%93%e8%89%b2%e4%bd%93%e6%8c%82%e8%bd%bd%e8%bd%af%e4%bb%b6\/","title":{"rendered":"\u6d45\u8c08\u4e00\u4e0b\u76ee\u524d\u51e0\u6b3e\u5e38\u7528\u7684\u67d3\u8272\u4f53\u6302\u8f7d\u8f6f\u4ef6"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"1891\" class=\"elementor elementor-1891\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-f3b0d59 e-flex e-con-boxed e-con e-parent\" data-id=\"f3b0d59\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-2e12fe2 elementor-widget elementor-widget-text-editor\" data-id=\"2e12fe2\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u81ea\u4ece2023\u5e74\u63a5\u89e6\u57fa\u56e0\u7ec4\u4ee5\u6765\uff0c\u5173\u4e8e\u67d3\u8272\u4f53\u6302\u8f7d\u7528\u8fc7\u4e86\u65e0\u6570\u4e2a\u8f6f\u4ef6\uff0c\u5305\u62ecjuice+3ddna\u3001haphic\u548cyahs\u3002\u63a5\u4e0b\u6765\u6211\u4f1a\u4f7f\u7528\u8fd9\u4e9b\u8f6f\u4ef6\u7684\u65f6\u95f4\u6765\u63cf\u8ff0\u6211\u5bf9\u8fd9\u4e9b\u8f6f\u4ef6\u7684\u611f\u53d7\uff0c\u5e76\u4e14\u4ece\u8f6f\u4ef6\u7684\u4e0b\u8f7d\u548c\u914d\u7f6e\u96be\u5ea6\u3001\u4f7f\u7528\u95e8\u69db\u3001\u8fd0\u884c\u901f\u5ea6\u548c\u8868\u73b0\u56db\u4e2a\u4e2a\u65b9\u9762\u7ed9\u51fa\u6211\u7684\u4e3b\u7ba1\u8bc4\u4ef7\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ce9fb24 elementor-widget elementor-widget-heading\" data-id=\"ce9fb24\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">1. juice+3ddna<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c7d0b0d elementor-widget elementor-widget-text-editor\" data-id=\"c7d0b0d\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u4f5c\u4e3a\u7b2c\u4e00\u4e2a\u63a5\u89e6\u7684\u67d3\u8272\u4f53\u6302\u8f7d\u8f6f\u4ef6\uff0c\u5f53\u65f6\u7684\u6211\u8fd8\u662f\u4e00\u4e2a\u5c0f\u767d\uff0c\u4e00\u8fb9\u770bGithub\u7684\u6559\u7a0b\u4e00\u8fb9\u53c2\u8003\u5f90\u5dde\u66f4\u8001\u5e08\u5199\u7684\u7b14\u8bb0\uff0c\u4e5f\u7b97\u662f\u5b8c\u6574\u7684\u8d70\u5b8c\u4e86\u6240\u6709\u7684\u6d41\u7a0b\u3002\u8fd9\u4e2a\u8f6f\u4ef6\u7ed9\u6211\u7684\u7b2c\u4e00\u5370\u8c61\u5c31\u662f\u201c<strong>\u9ebb\u70e6\uff01\u9ebb\u70e6\uff01\u9ebb\u70e6<\/strong>\u201d\uff0c\u5e76\u4e14\u5206\u6790\u65f6\u95f4\u975e\u5e38\u957f\uff0c\u5982\u679c\u662f\u57fa\u56e0\u7ec4\u6bd4\u8f83\u5927\uff0c\u751a\u81f3\u9700\u8981\u82b1\u4e0a\u6570\u5929\u4e43\u81f3\u4e00\u5468\u7684\u65f6\u95f4\u3002<\/p><p>\uff081\uff09\u914d\u7f6e\u96be\u5ea6\uff1a\u8f6f\u4ef6\u7684\u4e0b\u8f7d\u548c\u914d\u7f6e\u5bf9\u4e8e\u65b0\u624b\u6765\u8bf4\u4e5f\u6781\u5176\u4e0d\u53cb\u597d\uff0c\u5b8c\u5168\u4e0d\u652f\u6301conda\u4e0b\u8f7d\uff0c\u53ea\u80fd\u672c\u5730\u4e0b\u8f7d\uff0c\u7136\u540e\u914d\u7f6e\u3002<\/p><p>\uff082\uff09\u4f7f\u7528\u95e8\u69db\uff1a\u5177\u6709\u4e00\u5b9a\u7684\u95e8\u69db\uff0c\u6211\u81ea\u5df1\u5728\u4f7f\u7528\u7684\u8fc7\u7a0b\u4e2d\u51fa\u73b0\u8fc7\u591a\u6b21\u62a5\u9519\uff0c\u4f8b\u5982awk\u7248\u672c\u95ee\u9898\uff0culimit\u95ee\u9898\u7b49\u7b49\uff0c\u73b0\u5728\u6211\u8fd8\u8bb0\u5f97\u8f6f\u4ef6\u8981\u6c42HIC\u7684\u6d4b\u5e8f\u6570\u636e\u5fc5\u987b\u4e25\u683c\u6309\u7167_R1\u548c_R2\u7684\u683c\u5f0f\u6765\u624d\u884c\uff0c\u4e0d\u7136\u4f1a\u62a5\u9519\u3002<\/p><p>\uff083\uff09\u8fd0\u884c\u901f\u5ea6\uff1a\u8fd0\u884c\u901f\u5ea6\u5f88\u6162\uff0c\u8f83\u5927\u7684\u57fa\u56e0\u7ec4\u901a\u5e38\u9700\u8981\u8fd0\u884c\u51e0\u5929\u4e43\u81f3\u4e00\u5468\u3002<\/p><p>\uff084\uff09\u8868\u73b0\uff1a\u8868\u73b0\u8fd8\u7b97\u53ef\u4ee5\uff0c\u4f46\u662f\u5bf9\u4e8e\u591a\u500d\u4f53\u6216\u8005\u5355\u500d\u578b\u57fa\u56e0\u7ec4\u7684\u6302\u8f7d\u8868\u73b0\u4e0d\u8db3\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-925cfc0 elementor-widget elementor-widget-heading\" data-id=\"925cfc0\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">2. Haphic<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c73ee10 elementor-widget elementor-widget-text-editor\" data-id=\"c73ee10\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8fd9\u4e2a\u8f6f\u4ef6\u662f\u57fa\u56e0\u6240\u4faf\u5e08\u5144\u63a8\u8350\u6211\u4f7f\u7528\u7684\uff0c\u5e08\u5144\u548c\u6211\u8bf4\u8fd9\u4e2a\u8f6f\u4ef6\u8fd0\u884c\u901f\u5ea6\u5f88\u5feb\uff0c\u6211\u5c31\u53bb\u5c1d\u8bd5\u4e86\uff0c\u7ed3\u679c\u786e\u5982\u5e08\u5144\u6240\u8a00\uff0c\u5feb\u5230\u98de\u8d77\u3002<\/p><p>\uff081\uff09\u914d\u7f6e\u96be\u5ea6\uff1a\u76f4\u63a5Conda\u4e0b\u8f7d\u5373\u53ef\uff0c\u975e\u5e38\u65b9\u4fbf\uff0c\u4f46\u662f\u5728\u6211\u7684\u670d\u52a1\u5668\u4e0a\u4e0d\u80fd\u901a\u8fc7\u76f4\u63a5\u8f93\u5165\u8f6f\u4ef6\u7684\u4e3b\u7a0b\u5e8f\u6765\u8fd0\u884c\uff0c\u5fc5\u987b\u8981\u6307\u5b9a\u4e3b\u7a0b\u5e8f\u7684\u8def\u5f84\u624d\u53ef\u4ee5\u3002<\/p><p>\uff082\uff09\u4f7f\u7528\u95e8\u69db\uff1a\u57fa\u672c\u4e0a\u6ca1\u6709\u95e8\u69db\uff0c\u8ddf\u7740\u66fe\u8001\u5e08\u5728\u5b98\u7f51\u5199\u7684\u6559\u7a0b\u5c31\u53ef\u4ee5\u3002<\/p><p>\uff083\uff09\u8fd0\u884c\u901f\u5ea6\uff1a\u6781\u5feb\u3002<\/p><p>\uff084\uff09\u8868\u73b0\uff1a\u5bf9\u591a\u500d\u4f53\u548c\u5355\u500d\u578b\u57fa\u56e0\u7ec4\u8868\u73b0\u5f88\u597d\uff0c\u6b63\u5e38\u57fa\u56e0\u7ec4\u672a\u77e5\uff0c\u6ca1\u8bd5\u8fc7\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9e3ecfb elementor-widget elementor-widget-text-editor\" data-id=\"9e3ecfb\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p><strong>\u989d\u5916\u8865\u5145\u4e00\u70b9\uff1a\u8fd9\u4e2a\u8f6f\u4ef6\u5bf9\u4e8e\u4e0b\u6e38\u7684\u8c03\u6574\u6302\u8f7d\u7ed3\u679c\u7684Juicebox\u8854\u63a5\u975e\u5e38\u4f18\u79c0\uff0c\u4f5c\u8005\u76f4\u63a5\u4fee\u597d\u4e86sh\u811a\u672c\uff0c\u5e76\u4e14\u6709\u4e00\u4e9b\u5176\u4ed6\u4f18\u79c0\u7684\u5c0f\u529f\u80fd\uff0c\u5bf9\u4e8e\u591a\u500d\u4f53\u57fa\u56e0\u7ec4\u7684\u67d3\u8272\u4f53\u6302\u8f7d\u53ca\u5176\u63a8\u8350\uff01<\/strong><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-09d710f elementor-widget elementor-widget-heading\" data-id=\"09d710f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">3. Yahs<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-267c2e9 elementor-widget elementor-widget-text-editor\" data-id=\"267c2e9\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8fd1\u671f\u63a5\u89e6\u7684\u4e00\u4e2a\u8f6f\u4ef6\uff0c\u901f\u5ea6\u540c\u6837\u5feb\u7684\u98de\u8d77\uff0c\u4f46\u662f\u5bf9\u4e8e\u4e0b\u6e38Juicebox\u8c03\u6574\u7684\u8854\u63a5\u4e0d\u5982Haphic\u3002<\/p><p>\uff081\uff09\u914d\u7f6e\u96be\u5ea6\uff1a\u76f4\u63a5Conda\u4e0b\u8f7d\u5373\u53ef\uff0c\u975e\u5e38\u65b9\u4fbf\u3002<\/p><p>\uff082\uff09\u4f7f\u7528\u95e8\u69db\uff1a\u57fa\u672c\u4e0a\u6ca1\u6709\u95e8\u69db\uff0c\u4f46\u662f\u4e0b\u6e38\u8f6f\u4ef6\u7684\u8854\u63a5\u4e0d\u8db3\u3002<\/p><p>\uff083\uff09\u8fd0\u884c\u901f\u5ea6\uff1a\u6781\u5feb\u3002<\/p><p>\uff084\uff09\u8868\u73b0\uff1a\u6b63\u5e38\u57fa\u56e0\u7ec4\u7684\u8868\u73b0\u5f88\u597d\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8134e35 elementor-widget elementor-widget-text-editor\" data-id=\"8134e35\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p><strong>Yahs\u5b8c\u5168\u662fjuice+3ddna\u7684\u4e0a\u4f4d\u66ff\u4ee3\uff0c\u66f4\u5feb\uff01\u66f4\u51c6!\u66f4\u597d\uff01<\/strong><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4c13099 elementor-widget elementor-widget-heading\" data-id=\"4c13099\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">4. \u603b\u7ed3<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b88be63 elementor-widget elementor-widget-text-editor\" data-id=\"b88be63\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u591a\u500d\u4f53\u548c\u5355\u500d\u578b\u57fa\u56e0\u7ec4\u9996\u9009Haphic\uff0c\u6b63\u5e38\u57fa\u56e0\u7ec4\u9996\u9009Yahs\u3002\u63a5\u4e0b\u6765\u662fYahs\u7684\u4f7f\u7528\u6559\u7a0b\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fc3dedd elementor-widget elementor-widget-heading\" data-id=\"fc3dedd\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">5. Yahs\u8fdb\u884c\u67d3\u8272\u4f53\u6302\u8f7d<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-49925f7 elementor-widget elementor-widget-heading\" data-id=\"49925f7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">5.1 \u4e0b\u8f7d<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-320325a elementor-widget elementor-widget-code-highlight\" data-id=\"320325a\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>mamba install bioconda::yahs\r\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a73c9e5 elementor-widget elementor-widget-heading\" data-id=\"a73c9e5\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">5.2  \u4f7f\u7528<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f07a565 elementor-widget elementor-widget-code-highlight\" data-id=\"f07a565\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>### \u8fd9\u662f\u4e00\u4e2a\u7531\u4e09\u4e2a\u547d\u4ee4\u901a\u8fc7\u7ba1\u9053 (|) \u8fde\u63a5\u8d77\u6765\u7684\u547d\u4ee4\u6d41\uff0c\u7528\u4e8e\u5c06 Hi-C \u6d4b\u5e8f\u6570\u636e\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u8349\u56fe\u4e0a\uff0c\u5e76\u8fdb\u884c\u521d\u6b65\u8fc7\u6ee4\u3002\r\nbwa mem -5SP -t 28 purged.fa ..\/Chr\/fastq\/huangwenwucifeng_R1.fastq.gz ..\/Chr\/fastq\/huangwenwucifeng_R2.fastq.gz| samblaster | samtools view - -@ 14 -S -h -b -F 3340 -o HiC.bam\r\n\r\n# -5SP: \u8fd9\u662f\u4e24\u4e2a\u53c2\u6570\u7684\u7ec4\u5408\uff0c\u7279\u522b\u9002\u7528\u4e8e\u5904\u7406Hi-C\u6570\u636e\uff0c\u6709\u52a9\u4e8e\u5904\u7406\u5d4c\u5408\u8bfb\u957f\u5e76\u5f3a\u5236\u8fdb\u884c\u6b63\u786e\u7684\u53cc\u7aef\u914d\u5bf9\u3002\r\n# -t 28: \u6307\u5b9a\u4f7f\u7528 28 \u4e2a\u7ebf\u7a0b\u8fdb\u884c\u8ba1\u7b97\uff0c\u4ee5\u52a0\u5feb\u6bd4\u5bf9\u901f\u5ea6\u3002\r\n# purged.fa: \u8fd9\u662f\u53c2\u8003\u57fa\u56e0\u7ec4\u6587\u4ef6\uff08FASTA\u683c\u5f0f\uff09\uff0c\u5373contigs\u6216\u521d\u6b65\u7ec4\u88c5\u7684\u5e8f\u5217\u3002\r\n# ..\/Chr\/fastq\/huangwenwucifeng_R1.fastq.gz \u548c ..\/Chr\/fastq\/huangwenwucifeng_R2.fastq.gz: \u53cc\u7aef\u6d4b\u5e8f\u7684\u4e24\u4e2aFASTQ\u6587\u4ef6\uff08R1\u548cR2\uff09\u3002\r\n# |: \u7ba1\u9053\u7b26\u53f7\uff0c\u5c06\u524d\u4e00\u4e2a\u547d\u4ee4\u7684\u8f93\u51fa\u4f5c\u4e3a\u540e\u4e00\u4e2a\u547d\u4ee4\u7684\u8f93\u5165\u3002\r\n# samblaster: \u7528\u4e8e\u6807\u8bb0PCR\u91cd\u590d\u5e8f\u5217\u7684\u5de5\u5177\u3002\r\n# samtools view: SAMtools\u5de5\u5177\u96c6\u4e2d\u7684\u4e00\u4e2a\u547d\u4ee4\uff0c\u7528\u4e8e\u8f6c\u6362\u6bd4\u5bf9\u6587\u4ef6\u683c\u5f0f\u3002\r\n# -: \u8868\u793a\u4ece\u6807\u51c6\u8f93\u5165\uff08stdin\uff09\u8bfb\u53d6\u6570\u636e\uff0c\ufffd\ufffd\ufffd\u4ecesamblaster\u7684\u8f93\u51fa\u4e2d\u8bfb\u53d6\u3002\r\n# -@ 14: \u6307\u5b9asamtools\u4f7f\u752814\u4e2a\u7ebf\u7a0b\u3002\r\n# -S: \u6307\u5b9a\u8f93\u5165\u4e3aSAM\u683c\u5f0f\u3002\r\n# -h: \u5728\u8f93\u51fa\u4e2d\u5305\u542b\u5934\u4fe1\u606f\uff08header\uff09\u3002\r\n# -b: \u6307\u5b9a\u8f93\u51fa\u683c\u5f0f\u4e3aBAM\u3002\r\n# -F 3340: \u8fc7\u6ee4\u5668\u53c2\u6570\uff0c\u7528\u4e8e\u6392\u9664\u6807\u8bb0\u4e3a\u4e0d\u5408\u683c\u7684\u6bd4\u5bf9\u8bb0\u5f55\uff08\u5982\u672a\u6bd4\u5bf9\u3001\u975e\u4e3b\u8981\u6bd4\u5bf9\u3001\u91cd\u590d\u7b49\uff09\u3002\r\n# -o HiC.bam: \u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u540d\u4e3aHiC.bam\u3002\r\n\r\n### \u4f7f\u7528\u4e0a\u4e00\u6b65\u751f\u6210\u7684Hi-C\u6bd4\u5bf9\u4fe1\u606f\uff0c\u5bf9purged.fa\u4e2d\u7684contigs\u8fdb\u884c\u67d3\u8272\u4f53\u7ea7\u522b\u7684\u6302\u8f7d\u3002\r\nyahs .\/purged.fa aligned.bam\r\n\r\n# yahs: YAHS (Yet Another Hi-C Scaffolder) \u5de5\u5177\u7684\u4e3b\u547d\u4ee4\uff0c\u7528\u4e8e\u5229\u7528Hi-C\u6570\u636e\u8fdb\u884c\u57fa\u56e0\u7ec4\u6302\u8f7d\u3002\r\n# .\/purged.fa: \u8f93\u5165\u7684contigs\u6587\u4ef6\uff0c\u4e0e\u4e0a\u4e00\u6b65\u4e2d\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u662f\u540c\u4e00\u4e2a\u6587\u4ef6\u3002\r\n# aligned.bam: YAHS\u6240\u9700\u7684\u6bd4\u5bf9\u6587\u4ef6\uff08BAM\u683c\u5f0f\uff09\u3002\u6ce8\u610f\uff1a\u4e0a\u4e00\u4e2a\u547d\u4ee4\u751f\u6210\u7684BAM\u6587\u4ef6\u662f`HiC.bam`\uff0c\u8fd9\u91cc\u4f7f\u7528\u4e86`aligned.bam`\uff0c\u8bf7\u786e\u4fdd\u6587\u4ef6\u540d\u4e00\u81f4\u6216\u5df2\u505a\u76f8\u5e94\u5904\u7406\u3002\r\n\r\n### \u4f7f\u7528yahs\u7684\u8f93\u51fa\u7ed3\u679c\uff0c\u4e3aJuicer\u751f\u6210Hi-C\u63a5\u89e6\u56fe\u505a\u51c6\u5907\u3002\r\njuicer pre -a -o out_JBAT hic-to-contigs.bin scaffolds_final.agp contigs.fa.fai >out_JBAT.log 2>&1\r\n\r\n# juicer pre: Juicer\u5de5\u5177\u96c6\u7684\u7b2c\u4e00\u6b65\uff0c\u7528\u4e8e\u9884\u5904\u7406\u6570\u636e\u3002\r\n# -a: \u53ea\u5bf9AGP\u6587\u4ef6\u4e2d\u5217\u51fa\u7684contigs\/scaffolds\u8fdb\u884c\u57fa\u56e0\u7ec4\u5927\u5c0f\u7684\u4f30\u8ba1\u3002\r\n# -o out_JBAT: \u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00\u4e3aout_JBAT\u3002\r\n# hic-to-contigs.bin: yahs\u751f\u6210\u7684\u4e8c\u8fdb\u5236\u6587\u4ef6\uff0c\u5305\u542bHi-C\u94fe\u63a5\u4fe1\u606f\u3002\r\n# scaffolds_final.agp: yahs\u751f\u6210\u7684AGP\u6587\u4ef6\uff0c\u5b9a\u4e49\u4e86contigs\u5982\u4f55\u7ec4\u6210scaffolds\u3002\r\n# contigs.fa.fai: \u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u7d22\u5f15\u6587\u4ef6\uff08\u901a\u8fc7`samtools faidx`\u751f\u6210\uff09\u3002\r\n# >out_JBAT.log 2>&1: \u5c06\u6807\u51c6\u8f93\u51fa\u548c\u6807\u51c6\u9519\u8bef\u4fe1\u606f\u90fd\u91cd\u5b9a\u5411\u5230`out_JBAT.log`\u6587\u4ef6\u3002\r\n\r\n### \u4f7f\u7528Juicer Tools\uff0c\u6839\u636e\u9884\u5904\u7406\u6b65\u9aa4\u751f\u6210\u7684\u7ed3\u679c\u521b\u5efa.hic\u6587\u4ef6\u3002\r\n(java -jar -Xmx32G juicer_tools.1.9.9_jcuda.0.8.jar pre out_JBAT.txt out_JBAT.hic.part <(cat out_JBAT.log | grep PRE_C_SIZE | awk '{print $2\" \"$3}')) && (mv out_JBAT.hic.part out_JBAT.hic)\r\n\r\n# java -jar -Xmx32G juicer_tools.1.9.9_jcuda.0.8.jar pre: \u6267\u884cJuicer Tools\u7a0b\u5e8f\uff0c\u5e76\u5206\u914d\u6700\u592732GB\u5185\u5b58\u3002\r\n# out_JBAT.txt: `juicer pre`\u547d\u4ee4\u751f\u6210\u7684\u8f93\u5165\u6587\u4ef6\u5217\u8868\u3002\r\n# out_JBAT.hic.part: \u4e34\u65f6\u7684\u8f93\u51fa.hic\u6587\u4ef6\u3002\r\n# <(...): \u8fd9\u662f\u4e00\u4e2a\u8fdb\u7a0b\u66ff\u6362\uff0c\u5b83\u5c06\u62ec\u53f7\u5185\u547d\u4ee4\u7684\u8f93\u51fa\u4f5c\u4e3a\u4e00\u4e2a\u4e34\u65f6\u6587\u4ef6\u4f9b`juicer_tools`\u8bfb\u53d6\u3002\u8be5\u547d\u4ee4\u4ece\u65e5\u5fd7\u6587\u4ef6\u4e2d\u63d0\u53d6\u57fa\ufffd\ufffd\u7ec4\u5927\u5c0f\u4fe1\u606f\u3002\r\n# &&: \u903b\u8f91\u4e0e\u64cd\u4f5c\u7b26\u3002\u53ea\u6709\u5f53`java`\u547d\u4ee4\u6210\u529f\u6267\u884c\u540e\uff0c\u624d\u4f1a\u6267\u884c`mv`\u547d\u4ee4\u3002\r\n# mv out_JBAT.hic.part out_JBAT.hic: \u5c06\u4e34\u65f6\u7684.hic\u6587\u4ef6\u91cd\u547d\u540d\u4e3a\u6700\u7ec8\u7684\u8f93\u51fa\u6587\u4ef6\u3002\r\n\r\n### \u5bf9Juicer\u7684\u8f93\u51fa\u8fdb\u884c\u540e\u5904\u7406\uff0c\u751f\u6210\u6700\u7ec8\u7684\u7ec4\u88c5\u6587\u4ef6\u3002\r\njuicer post -o out_JBAT out_JBAT.review.assembly out_JBAT.liftover.agp contigs.fa\r\n\r\n# juicer post: Juicer\u7684\u540e\u5904\u7406\u6b65\u9aa4\u3002\r\n# -o out_JBAT: \u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00\u3002\r\n# out_JBAT.review.assembly: \u8f93\u5165\u7684\u7a0b\u5e8f\u96c6\u5ba1\u67e5\u6587\u4ef6\uff0c\u901a\u5e38\u662f\u5728Juicebox\u7b49\u5de5\u5177\u4e2d\u624b\u52a8\u5ba1\u67e5\u548c\u6821\u5bf9\u540e\u7684\u7ed3\u679c\u3002\r\n# out_JBAT.liftover.agp: Juicer\u751f\u6210\u7684AGP\u6587\u4ef6\uff0c\u7528\u4e8e\u5750\u6807\u8f6c\u6362\u3002\r\n# contigs.fa: \u539f\u59cb\u7684contigs FASTA\u6587\u4ef6\u3002\r\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-1d3e429 e-flex e-con-boxed e-con e-parent\" data-id=\"1d3e429\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>\u81ea\u4ece2023\u5e74\u63a5\u89e6\u57fa\u56e0\u7ec4\u4ee5\u6765\uff0c\u5173\u4e8e\u67d3\u8272\u4f53\u6302\u8f7d\u7528\u8fc7\u4e86\u65e0\u6570\u4e2a\u8f6f\u4ef6\uff0c\u5305\u62ecjuice+3ddna\u3001haphic\u548cyah &#8230; <a title=\"\u6d45\u8c08\u4e00\u4e0b\u76ee\u524d\u51e0\u6b3e\u5e38\u7528\u7684\u67d3\u8272\u4f53\u6302\u8f7d\u8f6f\u4ef6\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/07\/27\/%e6%b5%85%e8%b0%88%e4%b8%80%e4%b8%8b%e7%9b%ae%e5%89%8d%e5%87%a0%e6%ac%be%e5%b8%b8%e7%94%a8%e7%9a%84%e6%9f%93%e8%89%b2%e4%bd%93%e6%8c%82%e8%bd%bd%e8%bd%af%e4%bb%b6\/\" aria-label=\"\u9605\u8bfb \u6d45\u8c08\u4e00\u4e0b\u76ee\u524d\u51e0\u6b3e\u5e38\u7528\u7684\u67d3\u8272\u4f53\u6302\u8f7d\u8f6f\u4ef6\">\u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-1891","post","type-post","status-publish","format-standard","hentry","category-6"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>\u6d45\u8c08\u4e00\u4e0b\u76ee\u524d\u51e0\u6b3e\u5e38\u7528\u7684\u67d3\u8272\u4f53\u6302\u8f7d\u8f6f\u4ef6 - 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