{"id":268,"date":"2018-12-09T14:32:00","date_gmt":"2018-12-09T06:32:00","guid":{"rendered":"https:\/\/www.next-bioinfo.tw\/?p=268"},"modified":"2023-09-23T14:44:28","modified_gmt":"2023-09-23T06:44:28","slug":"%e3%80%903d-genome%e3%80%91-hic-pro-%e8%bc%b8%e5%87%ba%e6%aa%94allvalidpairs-%e7%9a%84%e6%a0%bc%e5%bc%8f%e7%ad%86%e8%a8%98","status":"publish","type":"post","link":"https:\/\/www.next-bioinfo.tw\/en\/2018\/12\/%e3%80%903d-genome%e3%80%91-hic-pro-%e8%bc%b8%e5%87%ba%e6%aa%94allvalidpairs-%e7%9a%84%e6%a0%bc%e5%bc%8f%e7%ad%86%e8%a8%98\/","title":{"rendered":"\u30103D Genome\u3011 HiC-Pro \u8f38\u51fa\u6a94allValidPairs \u7684\u683c\u5f0f\u7b46\u8a18"},"content":{"rendered":"<p><strong>allValidPairs<\/strong>\u6a94\u70baHiC Pro\u7684\u4e3b\u8981\u8f38\u51fa\u7d50\u679c\u4e4b\u4e00\uff0c\u57fa\u672c\u4e0a\u7d00\u9304\u4e86Hi-C\u77e9\u9663\u7684\u539f\u59cb\u8cc7\u8a0a\uff0c\u5f8c\u7e8c\u5206\u6790\u6b65\u9a5f\u4e2d\u4e5f\u53ef\u4ee5\u628a.allValidPairs\u8f49\u63db\u6210\u58d3\u7e2e\u683c\u5f0f.hic\u4f86\u8996\u89ba\u5316\u3002allValidPairs\u7684\u6bcf\u500brow\u4ee3\u8868\u5169\u500b\u4f4d\u7f6e\u6709interaction\u7684record\uff0c\u4e5f\u5c31\u662f\u7d00\u9304\u4e00\u7b46\u5be6\u9a57\u4e0a\u89c0\u6e2c\u5230\u7684cross linking pair\uff0c\u8981\u7522\u751fcontact matrix\u5247\u662f\u9084\u9700\u8981\u5728\u7522\u751f.hic\u7684\u904e\u7a0b(\u53ef\u4ee5\u7528HiC-Pro\u7684hicpro2juicebox.sh)\u5c07\u5176\u7e3d\u6578\u91cf\u7d71\u8a08\u8d77\u4f86\u3002<\/p>\n\n\n\n<p>\u4f8b\u5982\u4ee5\u4e0b\u8cc7\u6599\uff1a<\/p>\n\n\n\n<div class=\"wp-block-kevinbatdorf-code-block-pro\" data-code-block-pro-font-family=\"Code-Pro-JetBrains-Mono\" style=\"font-size:.875rem;font-family:Code-Pro-JetBrains-Mono,ui-monospace,SFMono-Regular,Menlo,Monaco,Consolas,monospace;line-height:1.25rem;--cbp-tab-width:2;tab-size:var(--cbp-tab-width, 2)\"><span role=\"button\" tabindex=\"0\" data-code=\"E00513:63:H2V37CCX2:8:2116:16498:70574  Chr1     1767    -       Chr1      8888    +       182     HIC_Chr1_8        HIC_Chr1_33       8       42      0-0\" style=\"color:#d8dee9ff;display:none\" aria-label=\"Copy\" class=\"code-block-pro-copy-button\"><svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" style=\"width:24px;height:24px\" fill=\"none\" viewbox=\"0 0 24 24\" stroke=\"currentColor\" stroke-width=\"2\"><path class=\"with-check\" stroke-linecap=\"round\" stroke-linejoin=\"round\" d=\"M9 5H7a2 2 0 00-2 2v12a2 2 0 002 2h10a2 2 0 002-2V7a2 2 0 00-2-2h-2M9 5a2 2 0 002 2h2a2 2 0 002-2M9 5a2 2 0 012-2h2a2 2 0 012 2m-6 9l2 2 4-4\"><\/path><path class=\"without-check\" stroke-linecap=\"round\" stroke-linejoin=\"round\" d=\"M9 5H7a2 2 0 00-2 2v12a2 2 0 002 2h10a2 2 0 002-2V7a2 2 0 00-2-2h-2M9 5a2 2 0 002 2h2a2 2 0 002-2M9 5a2 2 0 012-2h2a2 2 0 012 2\"><\/path><\/svg><\/span><pre class=\"shiki nord\" style=\"background-color: #2e3440ff\" tabindex=\"0\"><code><span class=\"line\"><span style=\"color: #88C0D0\">E00513:63:H2V37CCX2:8:2116:16498:70574<\/span><span style=\"color: #D8DEE9FF\">  <\/span><span style=\"color: #A3BE8C\">Chr1<\/span><span style=\"color: #D8DEE9FF\">     <\/span><span style=\"color: #B48EAD\">1767<\/span><span style=\"color: #D8DEE9FF\">    <\/span><span style=\"color: #A3BE8C\">-<\/span><span style=\"color: #D8DEE9FF\">       <\/span><span style=\"color: #A3BE8C\">Chr1<\/span><span style=\"color: #D8DEE9FF\">      <\/span><span style=\"color: #B48EAD\">8888<\/span><span style=\"color: #D8DEE9FF\">    <\/span><span style=\"color: #A3BE8C\">+<\/span><span style=\"color: #D8DEE9FF\">       <\/span><span style=\"color: #B48EAD\">182<\/span><span style=\"color: #D8DEE9FF\">     <\/span><span style=\"color: #A3BE8C\">HIC_Chr1_8<\/span><span style=\"color: #D8DEE9FF\">        <\/span><span style=\"color: #A3BE8C\">HIC_Chr1_33<\/span><span style=\"color: #D8DEE9FF\">       <\/span><span style=\"color: #B48EAD\">8<\/span><span style=\"color: #D8DEE9FF\">       <\/span><span style=\"color: #B48EAD\">42<\/span><\/span>\n<span class=\"line\"><span style=\"color: #D8DEE9FF\">      <\/span><span style=\"color: #88C0D0\">0-0<\/span><\/span><\/code><\/pre><\/div>\n\n\n\n<p>\u76f4\u63a5\u62c6\u89e3\u5982\u4e0b\uff1a<\/p>\n\n\n\n<div class=\"wp-block-kevinbatdorf-code-block-pro\" data-code-block-pro-font-family=\"Code-Pro-JetBrains-Mono\" style=\"font-size:.875rem;font-family:Code-Pro-JetBrains-Mono,ui-monospace,SFMono-Regular,Menlo,Monaco,Consolas,monospace;line-height:1.25rem;--cbp-tab-width:2;tab-size:var(--cbp-tab-width, 2)\"><span role=\"button\" tabindex=\"0\" data-code=\"read_name \/ chr_A \/ start_A \/ strand_A \/ chr_B \/ start_B \/ strand_B \/ insert size \/ fragment_name_A \/ fragment_name_B \/ mapQ_A \/ mapQ_B \/ allele-specific info\" style=\"color:#d8dee9ff;display:none\" aria-label=\"Copy\" class=\"code-block-pro-copy-button\"><svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" style=\"width:24px;height:24px\" fill=\"none\" viewbox=\"0 0 24 24\" stroke=\"currentColor\" stroke-width=\"2\"><path class=\"with-check\" stroke-linecap=\"round\" stroke-linejoin=\"round\" d=\"M9 5H7a2 2 0 00-2 2v12a2 2 0 002 2h10a2 2 0 002-2V7a2 2 0 00-2-2h-2M9 5a2 2 0 002 2h2a2 2 0 002-2M9 5a2 2 0 012-2h2a2 2 0 012 2m-6 9l2 2 4-4\"><\/path><path class=\"without-check\" stroke-linecap=\"round\" stroke-linejoin=\"round\" d=\"M9 5H7a2 2 0 00-2 2v12a2 2 0 002 2h10a2 2 0 002-2V7a2 2 0 00-2-2h-2M9 5a2 2 0 002 2h2a2 2 0 002-2M9 5a2 2 0 012-2h2a2 2 0 012 2\"><\/path><\/svg><\/span><pre class=\"shiki nord\" style=\"background-color: #2e3440ff\" tabindex=\"0\"><code><span class=\"line\"><span style=\"color: #88C0D0\">read_name<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">chr_A<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">start_A<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">strand_A<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">chr_B<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">start_B<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">strand_B<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">insert<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">size<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">fragment_name_A<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">fragment_name_B<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">mapQ_A<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">mapQ_B<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">\/<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">allele-specific<\/span><span style=\"color: #D8DEE9FF\"> <\/span><span style=\"color: #A3BE8C\">info<\/span><\/span><\/code><\/pre><\/div>\n\n\n\n<p><p>\u4f4d\u4f9d\u5e8f\u70ba:<\/p><ol> <li> read\u540d\u7a31  <\/li><li>A's chromosome number<\/li><li>A's start position<\/li><li>A`strand(transcription direction)<\/li><li>B's chromosome number<\/li><li>B's start position<\/li><li>B`strand(transcription direction)<\/li><li> insert size<\/li><li>A\u7684fragment\u540d\u7a31<\/li><li> B\u7684fragment\u540d\u7a31<\/li><li>A\u7684MAPQ Quality Score<\/li><li> B\u7684MAPQ Quality Score<\/li><li>\u7b49\u4f4d\u57fa\u56e0\u7684\u5176\u4ed6\u8cc7\u8a0a <\/li><\/ol><p>\u53c3\u8003\u8cc7\u6599:<\/p><p><a href=\"https:\/\/github.com\/nservant\/HiC-Pro\/issues\/426\">https:\/\/github.com\/nservant\/HiC-Pro\/issues\/426<\/a><span style=\"font-size: revert; background-color: var(--kenta-base-100); color: var(--kenta-content-base-color);\"> <\/span><\/p><\/p>","protected":false},"excerpt":{"rendered":"<p>allValidPairs\u6a94\u70baHiC Pro\u7684\u4e3b\u8981\u8f38\u51fa\u7d50\u679c\u4e4b\u4e00\uff0c\u57fa\u672c\u4e0a\u7d00\u9304\u4e86Hi-C\u77e9\u9663\u7684\u539f\u59cb\u8cc7\u8a0a\uff0c\u5f8c\u7e8c\u5206\u6790\u6b65 [&hellip;]<\/p>","protected":false},"author":1,"featured_media":269,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_mi_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"site-container-style":"default","site-container-layout":"default","site-sidebar-layout":"default","site-transparent-header":"default","disable-article-header":"default","disable-site-header":"default","disable-site-footer":"default","disable-content-area-spacing":"default","footnotes":""},"categories":[20],"tags":[25,27,26],"_links":{"self":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/268"}],"collection":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/comments?post=268"}],"version-history":[{"count":1,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/268\/revisions"}],"predecessor-version":[{"id":270,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/268\/revisions\/270"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media\/269"}],"wp:attachment":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media?parent=268"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/categories?post=268"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/tags?post=268"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}